Tsawa Khangtsen occupies prominent place in the religious history of Sera Jey Dratsang. Sera Theckchen Ling was established as per visionary instruction given by Jamgon Lama Tsongkhapa Rinpoche in the year 1407. At that time there emerged four Dratsangs, Monasteries, and of these, the Drom-teng Dratsang was this present (Tsawa) Khangtsen.

Kunkhyen Lodoe Rinchen Senge founded Sera Jey Dratsang in the year 1466. During the time Manjushri Emanation Jetsun Choekyi Gyaltsen assumed the principal responsibility as a Master scholar of Sera Jey Dratsang, the monks in the Drom-teng Dratsang also became his direct students and thence they joined Sera Jey Dratsang Sangha community.

The Sangha member increased as well as the scholarship and intellectual activities. The celebrated Master and scholar, Panchen Delek Nyima, who was the illustrious disciple of Jetsun Choekyi Gyaltsen, renamed it as the Tsawa Khangtsen. For centuries, countless number of realized Masters and erudite scholars who first entered this Khangtsen had completed their philosophical studies with distinction and later they travelled to all regions in Tibet making great contribution to the prosperity and success of Buddha Dharma and happiness and spiritual fulfilment of countless sentient beings. To name few of them:

Je Namdhag Dorjee became the 42nd Throne holder of Gandhen as the representative of Je Rinpoche. He was enthroned in the year 1668 and went on to serve in that position for over seven years.

Venerable Lobsang Tenzin became 60th Throne Holder of Gandhen. He became a tutor to His Holiness the 8th Dalai Lama and made tremendous contribution to the service of Buddha Dharma.

The successive reincarnation of Vajradhara, Dagri Dorjee Chang. The first reincarnation of Dagri Phabongkhapa Khenchen Gyatso Thaye joined this Khangtsen and completed his studies and later he served as a tutor to 8th Dalai Lama as well.

Since having born as gnas brtan gser be'u, Neten Ser Beu, one of the sixteen famous Sthavira or elders who preached Buddhist doctrine in the various mythical islands and continents of the Buddhist cosmology, during the time Buddha lived, the line of reincarnations continued to this day. As recorded in the biography, when Reting Trichen Tenpa Rabgye was in retreat at Phabongkha hermitage, he received vision and prophecy from Second Buddha Urgyen Rinpoche appeared from the center of Palden Lhamo's hairs. This was later revealed to Chaglung Pundita, etc, in his own words. Rinpoche gave both sutric and tantic teachings and initiations extensively in the holy spiritual land of Tibet, and was highly respected as the lineage holder of the complete Lamrim Teaching and numerous initiations, oral transmission.

His reincarnation, Kangyurwa Dagri Dorjee Chang Lobsang Choejor Gyatso; Third reincarnation, Vajradhara Dagri Lobsang Thupten Namgyal; Fourth reincarnation, Kangyurwa Vajradhara Dagri Lobsang Lungrig Gyatso Wangyal; Fifth reincarnation, Dagri Thupten Lhundup Tenpai Gyaltsen is currently active in serving the Buddha Dharma having successfully completed Lharam Debate Examinations - all of them successfully completed their Monastic studies with distinction as their predecessors; rose to become highest respected Masters of Gelugpa School and were the lineage holder of Yamantaka and Hayagriva Deity practices. Many erudite scholars and accomplished masters emerged from among the large number of close direct disciples and students.

A great authority on scriptural and philosophical treatise, the most respected master Geshe Jampa Thaye also entered this Khangtsen and successfully completed all the courses of studies and trainings. He travelled to the great seat of learning; Chamdo Geden Jampa Ling situated in the heart of Dokham, and introduced dialectics and philosophy courses of studies which resulted into manifold increase in the monk scholars joining the Monastery.

The Monastery produced several renowned scholars and masters. The Monastery gradually emerged as the most prestigious center of higher Buddhist studies known for its high intellectual standard and accomplishment among all the Monastic colleges in whole of Kham, Eastern and Amdo, North-Eastern Tibet. That this great Monastery later came to be acclaimed as the second greatest seat of learning in entire Tibet, is the result of the successful spiritual deeds of this Bodhisattva incarnation.