By establishing a fuzzy mathematical evaluation model based on physical and chemical indicators, this paper investigates the genetic toxic pollution of Chaohu Lake in 2016 through the micronucleus technology of the Vicia faba root tip and evaluates the water quality of Chaohu Lake. The results show that, in recent years, the overall water quality of the lakes around Chaohu has improved slightly, but the pollution levels of some areas (such as Nan Fei He and Shi Wu Li He) are still serious. The results can also provide a more reliable theoretical basis for the planning and management of environment protection.