A legend that attests to the position of Shannan(Lhokha) Prefecture in the annals of Tibetan history states that the human beings are the creation of union between a sacred monkey and women. According to archaeological findings and legends and ancient documents, people lived in this area up to four million years ago. A primitive civilization grew up in the Yarlung Valley and a field in the village of Sare near Tsetang Town, is said to be the first farming field in Tibet. The first king in Tibetan history, Nyatri Tsenpo, really a mere chief of the Yarlong tribe, began ruling over the Yarlung valley in the beginning of second century BC. He founded the Fan Kingdom and established a hereditary monarchy. During the reign of the ninth king, Budegong, agriculture flourished and he was able to mobilize the people to excavate canal, channelling water to irrigate the flatland.[8] A formal forming system came into existence during the reign of Yixiulie, the eleventh king, when he devised standard measurement units for allocating farmland and counting livestock. Six palaces were built in the region between the rule of the ninth and fifteenth kings.

Around the 6th century AD, the Yarlung Valley became a slavery society, smelting iron, copper and silver to produce weapons and other objects. The 31st king of Yarlung, Langrilunzan, was an expansionist and invaded neighbouring tribes, expanding the territory of Yarlung. The 32nd king, Songtsän Gampo conquered Subi Tribe, Yangtong tribe and many others and established the Tubo Regime, or the Tibetan Empire. Although transferred his capital city from Qiongjie to Lhasa, many of his descendant of the royal lineage still lived in the Lhokha region. He made Yungbulakang Palace his summer palace, which by this time was an important centre for Buddhism and the storage of Buddhist scriptures. In 641 AD, Gampo married Princess Wencheng of the Tang Dynasty.

During the Tubo Regime, a great number of irrigation projects developed along the Yarlong River and the Yarlung Tsangpo River, and with the increase of yaks and horses here there was dramatic development in agriculture. However, continued conflict led to endless famine and eventually the collapse of the Tubo regime. In 1253, Mengge, the emperor of Yuan Dynasty, invaded Tibet and united the squabbling tribes into an administrative region, controlled by the central government of Yuan Dynasty in Beijing. However, the dominant tribe in the Yarlung valley during this period was the Pazhu Dynasty and in 1322, Qiangqujianqun became the leader of the Pazhu and replenished agricultural activity in the region, funding irrigation works, cultivating lands, reconstructing roads, restoring houses and developing husbandry. Qiangqujiangqun founded the Naidong Dynasty which would last for 262 years, introduced the system of feudal serfdom and implemented a new government system with divisions known as Zong, established 13 of them in Naidong (the capital), Gonggar and so forth.

On May 23 of 1951, Lhokha Prefecture, together with the other prefectures signed an agreement with the central government of the People’s Republic of China for the peaceful liberation of Tibet. However, in 1959, the Lhoka/Shannan Prefecture was annexed to China by brutal force and the feudal serfdom system was abolished. Many monasteries were destroyed during the invasion and the Yungbulakang Palace was severely damaged.