In order to thoroughly discuss the interannual change regulations of the precipitation and reference evapotranspiration in Xinjiang area, the Mann-Kendall trend analysis and BG segmentation algorithm were applied to study the trend and mutation characteristics of the annual precipitation and reference evapotranspiration of 52 meteorological stations in Xinjiang area, calculated with the FAO-56 Penman-Monteith formula. Results show that, over the last 60 years, the annual precipitation is increasing and the annual reference evapotranspiration is decreasing in general; furthermore, the mutation of annual reference evapotranspiration is more frequent and complicated comparing with annual precipitation. The natural supply and demand condition of water resources for agriculture in Xinjiang area is inclined to improve, which is beneficial to agriculture development.