Since the State Council issued The Advice on Applying the Strictest Water Resources Control System in 2012，the rural economy has developed rapidly，and people’s demand for water resources and water environment is increasing. Being the most basic management unit in China，how can the villages and towns manage water resources effectively and reasonably have become an important issue in the current social development. This paper analyzes the problems of water resources management system in typical villages and towns by means of investigation in typical areas and comprehensive analysis based on the analysis of the characteristics of water resources，distribution of water conservancy projects and water resources management in villages and towns in Sichuan Province. Through the research，the study reveals that loopholes in water resources management are caused by regional differences in water resources which lead to differences in management systems，unclear responsibilities for villages and towns water resources management，lack of water resources management personnel，and dificient villages and towns water resources management systems. Therefore，some suggestions are put forward for improving the water resources management system，reasonably allocating the structure of water resources managers，and promoting the audit system of water resources asset in villages and towns. It has certain reference significance for the government to implement the strict water resources management system and the principle of “water saving priority”.