Internal strife in the Central Plains during the Five Dynasties period, and the Song, Liao and Jin dynasties distracted the attention of rulers of the Central Plains from the Western Regions, resulting in several local regimes existing side by side in the Western Regions. The local governments of Gaochang, Karahan and Yutian exercised a great degree of autonomy, but they all maintained close ties with the ruling dynasties in the Central Plains.

The Gaochang and Karahan were local regimes established by the Uighurs, who had moved west to the Western Regions together with other Turki-speaking tribes after the Mobei Uighur Khanate collapsed in 840. The Gaochang had the Turpan area as its center while the Karahan controlled the vast areas south of the Tianshan Mountains and Hezhong (Samarkand) in Central Asia.

The Uighur local regimes had very close relations with the ruling dynasties in the Central Plains. The ruler of the Karahan Kingdom called himself the "Peach Stone Khan," meaning "Chinese Khan," to indicate that he was a Chinese subject. In 1009, after occupying Yutian, Karahan sent envoys with tribute to the emperor of the Northern Song Dynasty (960-1127). In 1063, the Northern Song conferred upon the ruler of Karahan the title of "King of Sworn Allegiance." In the third year after the founding of the Northern Song Dynasty, the Gaochang Uighurs sent 42 envoys bearing tribute to the Northern Song court.

Yutian was the habitat of the Sai people. In recognition of its maintaining close ties with the Central Plains, the Tang Dynasty conferred an official title on the ruling clan of Yutian, which then changed its surname from Yuchi to Li, the surname of the Tang ruling house. In 938, Emperor Gaozu of the Later Jin Dynasty sent Zhang Kuangye and Gao Juhui to Yutian as envoys to confer on Li Shengtian, Yutian's ruler, the title of "King of the Great Treasure Yutian State." In the early years of the Northern Song Dynasty, envoys and monks from Yutian brought tribute to the Song Dynasty court from time to time.

The founder of the Yuan Dynasty, Genghis Khan, completed the political unification of the regions north and south of the Tianshan Mountains. He first set up military and administrative organs like "Dargaq" (a Mongolian official title, meaning "garrison officer") and "Bexibalik Secretariat" to take charge of the military and administrative affairs of the Western Regions. After the Yuan Dynasty was proclaimed, while giving attention to socio-economic development in the Western Regions, it appointed a judicial commissioner in the Turpan region. Later, a treasury and printing house for banknotes were established there, together with a Bexibalik Command to administer the Turpan area, which was garrisoned by soldiers of the vanquished Southern Song Dynasty army, who were also there to open up wasteland. At the same time, the Yuan court sent soldiers to Hotan and Qiemo for garrison and reclamation duties, set up a foundry in Bexibalik to make farm tools, and instituted a land tax system in the Uighur areas. In 1406, the Ming Dynasty set up a Hami Garrison Command, and appointed the heads of the leading families in Hami as officials to manage local military and administrative affairs, so as to keep the trade routes to the West open and bring the other areas of the Western Regions under its control.

The Qing government consolidated unified jurisdiction over the Western Regions. In 1757, the Qing imperial court crushed the long-standing Junggar separatist regime in the northwest. Two years later, it quelled a rebellion launched by the Islamic Aktaglik Sect leaders Burhanidin and Hojajahan, thus consolidating its military and administrative jurisdiction over all parts of the Western Regions. The post of Ili General was established in 1762 to exercise unified military and administrative jurisdiction over the regions both south and north of the Tianshan Mountains, with the headquarters in Huiyuan (in modern Huocheng County) and staffed with officials like supervisors, consultants, superintendents and commissioners. In accordance with the principle of "doing what is appropriate in the light of local conditions" and "exercising administration according to local customs," the Qing government adopted the system of prefectures and counties in the region north of the Tianshan Mountains inhabited by people of the Han and Hui ethnic groups, and maintained the local "Baeg system" (a Turki term for local officials) for the Uygurs in the Ili region and the region south of the Tianshan Mountains. Even in the latter region, however, the central government reserved the power to make official appointments and removals with the strict separation of religion from politics. It adopted the system of "Jasak" (a Mongolian term for governor) by conferring the hereditary 'titles of princes and dukes on Mongolians and the Uygurs in the Hami and Turpan regions. It also recruited officials from other ethnic groups besides the Manchus. In economic affairs, the Qing promoted the simultaneous development of farming and livestock breeding, with the emphasis on farming. It also reduced taxes and fixed quotas for financial subsidies. Xinjiang witnessed steady social and economic development under the Qing Dynasty.