[5][4] Unlike other Madhyamaka philosophers, Śāntarakṣita accepted Yogācāra doctrines like mind-only (cittamatra) and self-reflective awareness (svasamvedana), but only on the level of conventional truth.

[6][7] According to James Blumenthal, this synthesis is the final major development in Indian Buddhist philosophy before the disappearance of Buddhism from India (c. 12-13th centuries).

Some of his history is detailed in a 19th-century commentary by Jamgon Ju Mipham Gyatso drawn from sources like the Blue Annals, Buton and Taranatha.

According to Ju Mipham, Śāntarakṣita was the son of the king of Zahor (in east India around the modern day states of Bihar and Bengal).

[5] However, according to Tibetan sources like the Blue Annals, his first trip was unsuccessful and due to the activities of certain local spirits, he was forced to leave.

[5] Tibetan sources then state that Śāntarakṣita later returned along with a tantric adept called Padmasambhava who performed the necessary magical rites to appease the unhappy spirits and to allow for the establishment of the first Buddhist monastery in Tibet.

[13] According to Tibetan sources, Śāntarakṣita and his students initially focused on teaching the 'ten good actions' (Sanskrit: daśakuśalakarmapatha), the six paramitas (transcendent virtues), a summary of the Mahāyāna and 'the chain of dependent origination' (pratītyasamutpāda).

[15][12] Ju Mipham writes that when he came to Tibet, "he set forth the ten good virtues, the eighteen dhatus, and the twelve fold chain of dependent arising.

[17] Like other Indian Madhyamaka thinkers, Śāntarakṣita explains the ontological status of phenomena through the use of the doctrine of the "two truths": the ultimate (paramārtha) and the conventional (saṃvṛti).

While in an ultimate or absolute sense, all phenomena as seen by Madhyamaka as being "empty" (shunya) of essence or inherent nature (svabhāva), they can be said to have some kind of conventional, nominal or provisional existence.

[4] Thus, Śāntarakṣita incorporates the Yogācāra school's analysis into his Madhyamaka framework as a useful way of understanding conventional reality and as a stepping stone to the highest view of emptiness of all phenomena.

[4] His main known works include:[5] Śāntarakṣita's Tattvasaṅgraha (Compendium on Reality/Truth) is a huge and encyclopaedic treatment (over 3,600 verses distributed into 26 chapters) of the major Indian philosophic views of the time.

[24] In this text, Śāntarakṣita explains and then refutes many non-Buddhist views systematically, including Sāṅkhya's primordial matter Nyāya's creator god (Īśvara) and six different theories on the self (ātman).

Therefore, those who hold the reins of logic while riding the carriage of the two systems [Mādhyamika and Yogācāra], attain the stage of a true Mahāyānist.”[5] Samding Dorje Phagmo Mipham lists Śāntarakṣita's main Indian students as Kamalaśīla, Haribhadra and Dharmamitra.

[25] Furthermore, according to David Seyfort Ruegg, other later Indian scholars such as Vidyākaraprabha (c. 800 CE), Nandasri, Buddhajñāna(pāda), Jitāri, and Kambalapāda also belongs to this Yogācāra-Mādhyamaka tradition.

[26] Ju Mipham further states that this tradition was continued by Tibetan scholars such as Ngok Lotsawa, Chaba Chökyi Senge and Rongton Choje.

[27] In the late 19th century, Ju Mipham attempted to promote Yogācāra-Mādhyamaka again as part of the Rimé movement and as a way to discuss specific critiques of Je Tsongkhapa's widely influential philosophy.

[28] As part of that movement the 19th century Nyingma scholar Jamgon Ju Mipham Gyatso wrote the first commentary in almost 400 years about Śāntarakṣita's Madhyamakālaṅkāra.

According to his student Kunzang Palden, Mipham had been asked by his teacher Jamyang Khyentse Wangpo to write a survey of all the major Mahayana philosophic shastras for use in the Nyingma monastic colleges.