Abstract: Improving agricultural water use efficiency is of great significance for agricultural sustainable development and food security. Thus it is the premise of the strategies to improve agricultural water use efficiency which analyzes the status and spatial distribution characteristics. The super efficiency Data Envelopment Analysis method is applied to calculate the efficiency of agricultural water use in 31 regions of China. Results show that the regional difference of agricultural water efficiency is obvious and the overall value is low. In order to explore the deeper causes of agricultural water use efficiency, geographically weighted regression is used to analyze the spatial heterogeneity and contribution degree of factors, and some factors are observed including annual precipitation, agricultural water consumption ratio, diversity of agricultural products, water saving irrigation area and irrigation costs per acre. The conclusions are follows: The effective measures to improve the efficiency of agricultural water use in Xinjiang are to adjust the structure of water use and the planting structure; Strengthening the engineering construction such as water storage project, water interception project and water-saving project is the most effective way in South China; Heilongjiang should focus on the development and application of water saving technology; Shandong, Henan, Tianjin, Hebei, Beijing, Jilin, Liaoning and Shanghai need to take consideration of the natural endowments, water consumption structure, planting structure, water saving technology and economic factors together; It is inappropriate to raise the average irrigation fee per acre in southwest and northwest regions to improve water use efficiency. In a word, the research results are helpful to formulate different countermeasures for agricultural water use efficiency in different regions.