Based on the researches of water use efficiency in China and other countries, a water resource utilization efficiency assessment index system is proposed, which includes six kinds such as water use per 10,000 Yuan of GDP, removal variability of agriculture water resources utilization efficiency, per 10,000 Yuan of added industrial output value etc. By the cluster analysis of indicator data, it adopted protection pursuit model and Genetic algorithm Optimization to establish water resources utilization efficiency evaluation model. Studying on the 299 cities of China in 2006, it divided into five grades to analyze the regional discrepancy of water resources utilization efficiency, which showed the obvious difference. In addition, principal factor analysis has been proposed on the pre and post ten cities in the ranking of water resources utilization efficiency to provide the evidences for improving region efficiency.
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