In order to explore the impact of the comprehensive reform of agricultural water price on agricultural water use efficiency in Xinjiang and achieve the goal of agricultural water conservation, under the institutional framework of integrated reform of agricultural water prices, this paper summarizes the comprehensive agricultural water price reform models of Shaya County and Daheyanzi medium-sized irrigation areas, and use the super efficiency SBM model to calculate their agricultural water use efficiency. On the basis of summarizing the reform models of the two regions, the Tobit model was used to explore the main factors affecting the efficiency of agricultural water use in Xinjiang. Research has shown that the overall agricultural water use efficiency in the two regions shows a fluctuating upward trend. Precipitation, agricultural terminal water prices, and the implementation of reward and subsidy systems have a positive effect on agricultural water use efficiency, while the reform area and irrigation quota have a negative impact on agricultural water use efficiency.