In order to discuss the change of water resources security in Chongqing， a system dynamics model of Chongqing water resources security was established. Five different scenarios were designed to predict the development of Chongqing water resources security from 2006 to 2030. The results show that keeping the current development mode unchanged and not improving it is not conducive to the safe utilization of water resources in Chongqing. Just saving energy and emission reduction or reducing water use for industry and agriculture can not effectively improve the utilization of water resources. Only by strengthening environmental protection，and pollution abatement， improving industrial techndogy and industrial structure， promoting agricultural modernization， and strengthening point source pollution control can we improve the safety of water resources in Chongqing effectively and promote the coordinated development of economy， society and environment.