Based on the statistical data of Xinjiang from 1999 to 2014, the level of regional water resources carrying capacity, which takes water resources scarcity index, water resources pressure index and water footprint economic benefits as indictor, was evaluated by the water footprint of bottom-up generalization method. The results indicated that: all indicators of water resources scarcity carrying capacity were in growth trend. Water resources scarcity index increased to 1.03 in 2014 (dry year), which meant that water resources was of serious shortage. Under the premise of ecological requirements and food security, it was recommended to adjust the planting proportion of crops, increase industrial production with low water consumption and high output value, and alleviate the pressure of regional water resources carrying capacity through cross-regional water diversion and trade.