In order to quantitatively analyze and evaluate the spatial balance and spatial difference of water resources, the combined method of connection number and coupling coordination degree was used to evaluate the spatial balance of regional water resources. Considering the composite relationship of water resources, economic society and ecological environment, an evaluation index system for spatial balance of water resources composed of two systems of water resources carrying capcity and bearing pressure and 15 evaluation indexes was established. The weight of evaluation index was calculated by fuzzy analytic hierarchy process based on accelerating genetic algorithm, and a spatial balance evaluation method of water resources based on connection number and coupling coordination degree was proposed. Taking Anhui Province as an example, the results show that the evaluation method is reasonable when applied to the evaluation of water resources spatial balance, which can make up for the defect that the traditional coupling coordination degree can not reflect the uncertainty problem, and accurately reflect the coordination between systems and the overall development level.