In order to further explore the explicit evidence of the effect of environmental audit on environmental quality, based on the classic project of “Three Rivers and Three Lakes” water pollution prevention and control performance audit investigation, using the microcosmic data of water quality monitoring of key rivers of China Environmental Monitoring Station from 2006 to 2018, this paper makes an empirical analysis of the effect of government environmental performance audit on water pollution prevention and control by using such methods as double difference and obvious intermediary effect. The results show that the government environmental performance audit has indeed helped to improve the water quality of “Three Rivers and Three Lakes”, and the effect of Huaihe River and Liaohe River is particularly significant. It has improved the water quality mainly by promoting the prevention and control of domestic pollution sources, but failed to significantly promote the prevention and control of productive pollution sources to improve the water quality. Therefore, we should further strengthen the scope, depth, strength and frequency of government environmental performance audit, enhance the application of audit results, and increase the cost of environmental violations.