Fish are important consumers in the food web of lakes. Fish can have different diets and can therefore occupy multiple trophic levels in the food web, thereby strongly affecting aquatic organisms and environment through trophic cascade. In the present study, we first summarize the key mechanisms and methods of biomanipulation by regulating fish assemblage. We also consider the example of Kuilei Lake, a shallow lake located in the middle and lower reaches of the Yangtze River, to elaborate on the ecological effects of integrated biomanipulation, which combines the enhancement and release of planktivorous, carnivorous, and detrivorous fish species and the removal of omnivorous fish species. Our results demonstrated the positive effects of integrated biomanipulation in optimizing the fish assemblage, water quality, and submerged plant in such a shallow lake. In conclusion, the study summarizes the impact of fish community regulation in optimizing lake ecosystems and provides new ideas and means for lake restoration.