Culture-based fisheries (CBFs) in China are well developed in most lakes; however, an ecological approach is required to assess and improve them. This study aimed to describe the characteristics of the aquatic ecosystem of Lake Shangshe (Yangtze River Basin, China) and propose suggestions to improve CBF practices using an Ecopath with Ecosim model. Based on the direction of water flow and different product supply services, different practices were implemented in the 3 sub-lakes of Lake Shangshe (upper lake area, ULA; middle lake area, MLA; lower lake area, LLA) between 2014 and 2015. Asian carp (Hypophthalmichthys molitrix, H. nobilis, Cteno-pharyngodon idella, Cyprinus carpio) and bream (Megalobrama amblycephala, Parabramis pekinensis) were stocked at 30.0 and 50.0 t km(-2) in the ULA and MLA, respectively. In the LLA, the same fish species were stocked at 50.0 t km(-2) and millet grass Echinochloa sp. was planted. Water quality, including physicochemical parameters, was monitored in the 3 sub-lakes. Total phosphorus and chemical oxygen demand were significantly lower in the ULA than in the MLA and LLA. Ecotrophic efficiency values were noticeably high for most of the functional groups, except small pelagic fishes and cyanobacteria. Mixed trophic impact analyses demonstrated high fishing pressure on piscivorous fishes. The total mean transfer efficiency (TE) was 14.4%. The ratios of total primary production to total respiration, total primary production to total biomass, and total biomass to total throughput were 1.847, 46.131, and 0.008, respectively. In conclusion, the TE and ecosystem maturity of the aquatic ecosystem of Lake Shangshe were higher than those of other lakes in China, with the trialed CBF practices having a positive effect on both factors.