He wrote commentaries on three different schools of Indian philosophy, Vedānta, Sāṃkhya, and Yoga, and brought them together into a single theistic synthesis known as avibhagādvaita ("indistinguishable non-dualism"). Although his sub-commentary on the Yoga Sutras, the Yogavarttika, is now his most widely read work, his earliest works belonged to the school of Bhedābheda (Difference and Non-difference) Vedanta. Like many medieval Vedāntins, he considers Shankara's school of Advaita Vedānta a school of Buddhism in disguise, and understands the phenomenal world as real instead of illusory. As Vijñānabhikṣu claims that all three of the schools he commented on were a unity, this leads him to make some controversial claims (for instance, that the originator of the Sāṃkhya philosophical system believed in the existence of God).
... certain thinkers began to treat as a single whole the diverse philosophival teachings of the Upanishads, epics, Puranas, and the schools known retrospectively as the "six systems" (saddarsana) of mainstream Hindu philosophy.
The tendency of "a blurring of philosophical distinctions" has also been noted by Burley. Lorenzen locates the origins of a distinct Hindu identity in the interaction between Muslims and Hindus, and a process of "mutual self-definition with a contrasting Muslim other", which started well before 1800. Both the Indian and the European thinkers who developed the term "Hinduism" in the 19th century were influenced by these philosophers.
Little good work has been written in English on Vijñānabhikṣu, and most of the texts in his large corpus have yet to be edited and published in Sanskrit, let alone translated into English.
- Vijnanamritabhashya ("The Nectar of Knowledge Commentary", commentary on Badarayana's Brahma Sutras)
- Ishvaragitabhashya ("Commentary on the Ishvara Gita")
- Sankhyasara ("Quintessence of the Sankhya")
- Sankhyasutrabhashya ("Commentary on the Sankhya Sutras" of Kapila)
- Yogasarasamgraha ("Compendium on the Quintessence of Yoga")
- Yogabhashyavarttika ("Explanation of the Commentary on the Yoga Sutras" of Vyasa)
- Ganganatha Jha, Yogasarasamgraha of Vijnanabhiksu, New Delhi: Parimal Publications, 1995.
- José Pereira, Hindu Theology: A Reader, Garden City: Doubleday, 1976. Includes translated excerpts from Vijnanamritabhashya and Sankhyasutrabhashya.
- T.S. Rukmani, Yogavarttika of Vijnanabhiksu, New Delhi: Munshiram Manoharlal, 1981.
- Nandalal Sinha, The Samkhya Philosophy, New Delhi: Oriental Books Reprint Corporation, 1979. Contains a complete translation of Vijnanabhikshu's Sankhyasutrabhashya.
- Shiv Kumar, Samkhyasara of Vijnanabhiksu, Delhi: Eastern Book Linkers, 1988.
- Burley, Mikel (2007), Classical Samkhya and Yoga: An Indian Metaphysics of Experience, Taylor & Francis
- Lorenzen, David N. (2006), Who Invented Hinduism: Essays on Religion in History, Yoda Press
- Nicholson, Andrew (2007), "Reconciling Dualism and Non-Dualism: Three Arguments in Vijñānabhikṣu’s Bhedābheda Vedānta", Journal of Indian Philosophy 35(3), 2007, pp. 371-403
- Nicholson, Andrew J. (2010), Unifying Hinduism: Philosophy and Identity in Indian Intellectual History, Columbia University Press
- Daniel P. Sheridan, "Vijnanabhikshu", in Great Thinkers of the Eastern World, Ian McGready, ed., New York: Harper Collins, 1995, pp. 248–251.