Groundwater resources is an important part of whole water resources in the west of China. Scientific investigation and evaluation for underground water is the basic work to resolve water resources problem. The water balance method is often used in groundwater resources evaluation. In this paper, the numerical simulation method was used to evaluate groundwater resources of Tarim Basin after the water balance method. Through the balance of groundwater resources method, groundwater was a positive equilibrium, and through the numerical simulation method, groundwater was a negative equilibrium. By comparing and analyzing, the water balance method can be evaluated facilities in large areas. But it can not be evaluated local area easily. Because there were many recharge items due from supply coefficient. The numerical simulation method can be evaluated all kinds of region, big or small. But, it needed more particular data. The numerical simulation process depended on exact hydrogeological conditions. The results were close to the realty than the water balance method. The two methods combined use for groundwater resources evaluation was better than one. It evaluated and analyzed the groundwater resource in Shaya County which purpose was scientific and reasonable exploitation and utilization of groundwater kept soil and water balance and promoted sustainable development of economy in Shaya County.