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Contrary to popular belief, the term "Semu" (interpreted literally as "color-eye") did not imply that caste members had "colored eyes" in contrast with black-eyed Mongol Yuan people. It in fact meant "assorted categories" (各色名目, gè sè míng mù), emphasizing the ethnic diversity of Semu people.
They had come to serve the Yuan Khanate by enfranchising under the dominant Mongol caste. The Semu were not a self-defined and homogeneous ethnic group per se, but one of the four castes of the Yuan dynasty: the Mongol, Semu (or Semuren), Han Chinese (Hanren in Chinese) and Manji (Nanren in Chinese). Among the Semu were Buddhist Turpan Uyghurs, Tanguts and Tibetans; Nestorian Christian tribes like the Ongud ; Alans; Muslim Central Asian Persian and Turkic peoples including the Khwarazmians and Karakhanids.
While administratively classified as Semu, many of these groups rather referred to themselves by their self-aware ethnic identities in everyday life, such as Uyghur. Muslims, Persians, Karakhanids and Khwarazmians in particular, were actually mistaken to be Uyghurs or at least, "from the land of the Uyghurs". Therefore they adopted the label conferred to them by the Chinese: "Huihui" (see Hui), which was a corruption of the name Uyghur, but at the same time distinguishable from the name reserved for Buddhist Turpan Uyghurs proper, "Weiwuer". Of the many ethnic groups classified as "Semu" during the Yuan, only the Muslim Hui managed to survive into the Ming period as a large collective identity with self-awareness of common identity spanning across the whole China.
Other ethnic groups were either small and confined to limited localities (such as the Buddhist Turpan Uyghurs in Wuling, Hunan, and the Babylonian Jewry of Kaifeng, see Kaifeng Jews), or were forced to assimilate into the Han Chinese or Muslim Huis (such as some Christian and Jewish Semu in the Northwest, who, though thoroughly Islamicized, still unto this day retain peculiar labels like "Black Cap/Doppa Huihui", "Blue Cap Huihui").
The historian Frederick W. Mote wrote that the usage of the term "social classes" for this system was misleading and that the position of people within the 4 class system was not an indication of their actual social power and wealth, but just entailed "degrees of privilege" to which they were entitled institutionally and legally so a person's standing within the classes was not a guarantee of their standing, since there were rich and well socially standing Chinese while there were less rich Mongol and Semu than there were Mongol and Semu who lived in poverty and were ill treated.
The reason for the order of the classes and the reason why people were placed in a certain class was the date they surrendered to the Mongols, and had nothing to do with their ethnicity. The earlier they surrendered to the Mongols, the higher they were placed, the more the held out, the lower they were ranked. The Northern Chinese were ranked higher and Southern Chinese were ranked lower because southern China withstood and fought to the last before caving in.  Major commerce during this era gave rise to favorable conditions for private southern Chinese manufacturers and merchants.
When the Mongols placed the Uighurs of the Kingdom of Qocho over the Koreans at the court the Korean King objected, then the Mongol Emperor Kublai Khan rebuked the Korean King, saying that the Uighur King of Qocho was ranked higher than the Karluk Kara-Khanid ruler, who in turn was ranked higher than the Korean King, who was ranked last, because the Uighurs surrendered to the Mongols first, the Karluks surrendered after the Uighurs, and the Koreans surrendered last, and that the Uighurs surrendered peacefully without violently resisting. Koreans were ranked as Han people along with northern Chinese.
Japanese historians like Uematsu, Sugiyama and Morita criticized the perception that a four class system existed under Mongol rule and Funada Yoshiyuki questioned the very existence of the Semu as a class.
Among the Huihui, or Hui, there were in fact Muslim lineages that have migrated to China via Central Asia or by sea route prior to the Yuan migration of merchants, adventurers, craftsmen and service men from the Muslim World to China. These Muslims were not previously known as Hui, but have come to associate themselves with the "Muslims from the land of the Uyghurs" by the mere fact of common religious identity. "Hui" has thus become synonymous with the Islamic religion in the Chinese language since the Ming period (but not before that). Besides identifying themselves as Huis, the Semu Muslims of the Yunnan province, especially those descended from the Khwarazmian statesman Sayyid Ajjal Shams al-Din Omar, or Sayyid Ajjal, came to be labeled as Panthay wherever they migrated to in Southeast Asia, including Myanmar and Thailand.
This name Panthay is particular to the Yunnan Huis and is not shared by Huis in other parts of China such as Fujian and Ningxia. Zheng He is probably the best-known Panthay Hui in the West. The learned Semu, including scribes, interpreters and statesmen who served the Mongol military class, were known for their contributions to Chinese literature and sciences. Many of them became masters of Chinese poetry and also helped compose state-commissioned historical works on previous dynasties. Their privileged position in the Yuan bureaucracy was in part due to the Mongol military class's distrust of the native Khitay and Manji subjects. One such Yuan Semu mandarin and poet was Guan Yunshi, a Turk of disputed origin.
After the fall of the Yuan, many Semu intellectuals, soldiers, due to their less entrenched loyalty to the Mongols, also became quickly assimilated into the Ming political culture and became prominent mandarins and aristocrats. Some no longer retained separate ethnic identity and became Han Chinese, others still served the Ming court as Muslim Huis. The Ming court's tolerance for loyal Muslims and respect for their practices and ethnic identity partially explains the strength and vitality of the Muslim Hui community in modern China, compared to other Semu groups such as the Christians and Jews.
Similar practices in other areas of the Mongol Empire
At the same time the Mongols imported Central Asian Muslims to serve as administrators in China, the Mongols also sent Han Chinese and Khitans from China to serve as administrators over the Muslim population in Bukhara in Central Asia, using foreigners to curtail the power of the local peoples of both lands.
Genghis Khan and the following Yuan emperors forbade Islamic practices like Halal butchering, forcing Mongol methods of butchering animals on Muslims, and other restrictive degrees continued. Muslims had to slaughter sheep in secret. Genghis Khan directly called Muslims and Jews "slaves", and demanded that they follow the Mongol method of eating rather than the halal method. Circumcision was also forbidden. Jews were also affected, and forbidden by the Mongols to eat Kosher. Toward the end, corruption and the persecution became so severe that Muslim Generals joined Han Chinese in rebelling against the Mongols. The Ming founder Zhu Yuanzhang had Muslim Generals like Lan Yu who rebelled against the Mongols and defeated them in combat. Some Muslim communities had the name in Chinese which meant "barracks" and also mean "thanks"; many Hui Muslims claim it is because that they played an important role in overthrowing the Mongols and it was named in thanks by the Han Chinese for assisting them.
The Muslims in the semu class also revolted against the Yuan dynasty in the Ispah Rebellion but the rebellion was crushed and the Muslims were massacred by the Yuan loyalist commander Chen Youding.
Around 1376 the 30 year old Chinese merchant Lin Nu visited Ormuz in Persia, converted to Islam, and married a Semu girl (“娶色目女”) (either a Persian or an Arab girl) and brought her back to Quanzhou in Fujian. The Confucian philosopher Li Zhi was their descendant. This was recorded in the Lin and Li geneaology《林李宗谱》.
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