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He studied medicine at the University of Edinburgh Medical School, graduating MD in 1858 with a thesis on phthisis. He served as a surgeon in the Crimean War, then went with his regiment to China and resigned his commission to join the Chinese army of General Charles Gordon which was subduing the Taiping rebels. He decided to make his home in China and married the niece of Chinese politician Li Hongzhang in December 1864. He became a civil servant of the Chinese imperial government, first in China and then in England. His first wife was a near relative of Lar Wang (納王郜雲官), one of the leaders of the Taiping rebellion. They had three sons and a daughter;:2-3 the eldest son, George, served as the British representative in Kashgar for 28 years. The Macartneys lived in Nanjing until 1876 when Macartney left for London to serve as secretary to successive Chinese ministers at the Court of St James. His wife stayed behind and died two years later.:3
He re-married in 1884 Jeanne Léon du Satoy, daughter of Jacques Léon du Sautoy, of Fontainebleau. Lady Macartney died at Hove, near Brighton, on 9 September 1902, and was interred at Dundrennan Abbey, Kirkcudbrightshire, Scotland seven days later. Sir Halliday died in 1906 at his home, Kenbank, St John's Town of Dalry and was also buried at Dundrennan Abbey.
- Boulger, Demetrius Charles; Crichton-Browne, James, Sir (1908). The life of Sir Halliday Macartney. London: J. Lane.
- "OBITUARY: SIR HALLIDAY MACARTNEY, K.C.M.G., M.D". BMJ. 1 (2372): 1442–1443. 1906. doi:10.1136/bmj.1.2372.1442-c. ISSN 0959-8138.
- Skrine, Sir Clarmont Percival; Nightingale, Pamela (1973). Macartney at Kashgar: new light on British, Chinese and Russian activities in Sinkiang, 1890-1918. London: Methuen.
- Macartney, Samuel H. (1858). Pathology of phthisis and its relation to fatty liver (MD thesis). The University of Edinburgh. hdl:1842/26705.
- "Li Hung Chang's Godson". Sevenoaks Chronicle and Kentish Advertiser. 23 April 1909. Retrieved 30 August 2015 – via British Newspaper Archive. (Subscription required (help)).
- "Deaths". The Times (36871). London. 12 September 1902. p. 1.
- "Court Circular". The Times (36773). London. 21 May 1902. p. 9.
- "No. 27471". The London Gazette. 5 September 1902. p. 5751.