Nagqu has a long history. In the 1950s numerous stone artifacts have been discovered in the northern Tibet Plateau, which reflects that the nomadic culture of the area can date back to the mid-18th century. According to historical records, this part of the world was originally controlled by the Zhangzhong polity. In Chinese sources it is referred to as “Yangtong”, while in Tibetan historical records it is called “Chodai” which means "herding tribe." Residents of Chodai are called "Changpa" meaning “northerners”, or "Changri" meaning “northern tribe”. At the peak of the Zhangzhong polity, the area was divided into three sections: interior, central and exterior. Today's Nagqu Prefecture covers the former central and exterior Zhangzhong. Around the 7th century, the eastern area came under the domination of the Supi tribe as Zhangzhong diminished in size towards the west. When the Tubo tribe later unified the whole of Tibet and founded the Tubo Kingdom, northern Tibet was incorporated into its sphere of influence.
During the reign of the Tubo king Songtsan Gambo, Tubo was composed of four "tai"(terms used to describe area of administration) and 61 "domdai" (equivalent to 1,000-household offices). "Sumboru" was established in the area formerly under the tribe as the base for the Tubo as they expanded into the western regions. According to historical records, "half of the military food grain and horses came from the area."
After 1279, Nagqu became one of the Four Northern Tribes, which also incorporated Yangbajain, Bamcang (today's Tangra Yumco Lake area) and Langru (today’s Pangkog County). In 1269, Kublai Khan, who later established the Yuan Dynasty, sent his officials to set up post stations on the major postal routes from Qinghai to Sasgyia.. The postal routes extended through present-day Baqen, Sog, Biru, Nagqu and Damzung. Mongolian troops stationed in northern Tibet, and the Mongolian forces known as the Tribe Hor were gradually established in the area.
In 1725, the Qing (1644-1911) government appointed an official to Qinghai to administer local affairs. The 12th "king of Hor" was put in charge of the Hor area under the leadership of the Ethnic Affairs Office of the Qing Commission for Mongolian and Tibetan Affairs. In 1728, the Qing government established the High Commissioner Office in Lhasa, and three years later made moves to determine the border between Qinghai and Tibet. In 1731, the tribes in the southern Tanggula Mountains and the Tribe Hor came under the control of the Qing High Commissioner the tribes in the northern Tanggula Mountains came under the control of the Minister for Qinghai. In the same year, a population census was conducted among the various tribes. By 1907, the 33rd year of the reign of the Qing emperor Guangxu, eight generations of "Hor kings" had been granted official positions by the Qing government.
In 1751, when the Qing govenment sent troops to frustrate the plot engineered by Gyurmed Namugyal(who attempted to seize the power from the Hor), the government implemented a 13-article Ordinance for the more effective governing of Tibet, which included a major reform of the administrative system. Given the geographical location of Nagqu and its strategic importance for the suppression of riots in Tibet, the Qing government established Kamxian County which followed the temporal and religious administration. Part of Nagqu was controlled by the Panchen Erdeni.
During the Revolution of 1911, the Qing government was toppled. This made it possible for the Gaxag government to take over area directly under the Qing High Commissioners and the Hor area. When the 9th Panchen Erdeni was forced to exile, the Gaxag government forcibly seized control of area formerly controlled by the Panchen Erdeni. For the first time following the fall of Tubo Kingdom, northern Tibet became unified under the Gaxag government. In order to tighten control of the area, the Gaxag government installed Horkyi (the title for the highest officer in the area). This put an end to the 500-year history of 21 Hor kings. There were nine Horkyis in history. In 1942, the Gaxag government rescinded the post of Horkyi, and installed the Nagqu Administration in northern Tibet and ruled over the pastoral area in northern Tibet and the 14 counties north of Lhasa. By 1959, there were five generations of Nagqu chief managers. Each was of fourth ranking official position, and each position was shared by one monk and one lay official.
In October 1950, Chamdo and eastern Nagqu won liberation. The Qamdo people's Liberation Committee was established in March of the following year. Counties formerly under Nagqu Administration, including Nyainrong, Sog, Baqen, Biru, Xainza and Dengqen, came under the control of the first office of the Liberation Committee stationed in Dengqen. After the signing of the 17-article Agreement for the Peaceful Liberation of Tibet in 1951, some 2,000 members of the main force of the PLA 18th Army escorted the 10th Panchen Erdeni back to Tibet via northern Tibet. Nagqu, which was formerly under the control of the Panchen was naturally returned to him. January 1953 saw the founding of the CPC Tibet Work Committee and the Hehei Branch Committee. On October 9th, 1956, the Preparatory Committee of the Tibet Autonomous Region established the Heihe Kyicho Office.
After the democratic reform of 1959, the Heihe Prefecture and the Heihe County governments were set up. In 1960, the State Council authorized the change of name from Heihe prefecture and county to the Nagqu prefecture and county. Today, the Nagqu Town has developed into a prosperous city with over 10,000 residents and thousands of transient population. With new streets around many buildings and comprehensive social service facilities, Nagqu has become a centre of politics, economy, culture and transportation in northern Tibet.