Abstract: To reveal the influence of the environmental governance project on aquatic ecosystem health of Lihu Lake, an aquatic ecosystem health comprehensive index (EHCI) system was developed by physicochemical indexes and ecological indexes, and weight coefficient of each index was established based on entropy weight method. The results showed that the aquatic EHCI was between 21.65 and 72.74 during 1992-2012, which mainly decreased first and then rose remarkably. The health level increased from grade Ⅳ“poor” in 2003 to gradeⅡ“good” in 2012 after the implementation of environmental governance project since 2003. Spatially, the aquatic ecological health level in West Lihu Lake was better than that in East Lihu Lake, especially in the returning fishery to lake area (Area A), which was close to gradeⅠ“very good”. However, due to less management engineering, Area D was worse and was still in grade Ⅲ “medium”. The evaluation results conformed to the actual survey results for aquatic ecosystem in each area of Lihu Lake. The method can provide reference for aquatic ecological health evaluation of other similar lakes.