The Qing government introduced a system of local military command offices in Xinjiang. It appointed the General in Ili as the highest Western Regional Governor of administrative and military affairs over northern and southern Xinjiang and the parts of Central Asia under Qing influence and the Kazak and Blut (Kirgiz) tribes. For local government, a system of prefectures and counties was introduced.
The imperial court began to appoint and remove local officials rather than allowing them to pass on their titles to their children. This weakened to some degree the local feudal system. The court also encouraged the opening up of waste land by garrison troops and local peasants, the promotion of commerce and the reduction of taxation, which were important steps in the social development of Uygur areas.
Xinjiang was completely under Qing Dynasty rule after the mid-18th century. Although political reforms had limited the political and economic privileges of the feudal Bokes (lords), and taxation was slightly lower, the common ethnic people's living standards did not change significantly for the better. The Qing officials, through local Bokes, exacted taxes even on "garden trees." The Bokes expanded ownership on land and serfs, controlled water resources and manipulated food grain prices for profit.