Abstract: The food web is a network that describes the complex nutritional interactions between different organisms in a biological community and reveals the substance circulation and energy flow in the ecosystem. Stable isotope analysis is one of the effective technology for studying the substance circulation and energy flow. This research applied carbon and nitrogen stable isotope analysis combined with theoretical fish diet and model prediction to construct the food web structure and quantify the energy transfer in Bao’an Lake. Our results showed that the main trophic level of fish species ranged from 2.1 to 3.3. Among the 16 fish species, the carnivorous fish species were the less and the omnivorous fish species were the most. The food web of Bao’an Lake mainly composed of two nutrient transmission pathways, the planktonic food chain with POM and phytoplankton as the main food sources and the benthic food chain with sediment as the main food source. POM, phytoplankton, zooplankton, and zoobenthos were the main food sources of fish in Bao’an Lake, followed by sediments and macrophyte, etc. In addition, the theoretical food web based on dietary data and the food web structure predicted by the BIMM indicated that the planktonic food chain was the dominant in the food web, and the importance of the benthic food chain in food web was low. Therefore, the food web regulation recommendations for Bao’an Lake to reduce the risk of algae bloom are: (1) Increase the number of filter-feeding fish, and use its active filter feeding habit to directly reduce phytoplankton; (2) Increase the number of carnivorous fish to reduce the omnivorous fish, and increase the volume of zooplankton; (3) Increase the number of large filter-feeding zoobenthos, and use their passive filter feeding habit to filter and reduce the volume of phytoplankton.