In order to realize the water resources sustainable utilization and implement the most stringent water resources management policy, it is important to establish the evaluation system. The “Three Red Lines” of water resources management was selected as reference to establish the evaluation system for water resources management in Chongqing, China on the basis of the existing research. The control indexes of water resources exploitation and utilization, water consumption efficiency and assimilative capacity of water function zone were quantified and, additionally, the computing methods of each evaluation index and the comprehensive score were discussed. In 2012, the system was applied to the thirtyeight counties in Chongqing. The results show that the appliance of evaluation system can effectively check the comprehensive management level of water resources development, water saving and water quality of the counties in Chongqing. Thus, it can provide effective appraisal method to implement the most stringent water resources management policy.