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Xinjiang is located in arid northwestern China where water cycle has accelerated due to increased precipitation and temperature. However, the regional water budget characteristics vary due to the complex topography and spatial heterogeneities of hydroclimatology. This study uses atmospheric forcing constrained by observation from 90 meteorological stations in Xinjiang as input for the optimized Community Land Model version 3.5 (CLM 3.5) to investigate Xinjiang’s regional water budgets from 1951 to 2000 between the northern and southern part divided by the Tianshan Mountain. Results show that precipitation, evapotranspiration and runoff increased in Xinjiang from 1951 to 2000, particularly after the climate shift around 1987, and the net water flux (P-E) gap between North and South Xinjiang was widened. Rapid, intense wetting occurred in North Xinjiang in response to regional climate change, whereas South Xinjiang experienced relatively small changes. North and South Xinjiang exhibited opposite trends in water table depth (WTD), which became shallower in North Xinjiang, particularly after 1987. The WTD in South Xinjiang gradually became deeper. These results suggest that water resources in North Xinjiang are more sensitive to the warmer and wetter climate than South Xinjiang, and the serious water shortage in South Xinjiang did not improve during the second half of the twentieth century.