Abstract: Dianchi Lake is the largest plateau lake in Yunnan Province. To restore the health of its fish ecosystem, based on 2023 fishery resource survey data and an analysis of the current status of aquatic organisms, we constructed an Ecopath model to simulate changes in energy flow efficiency and fish species diversity before and after the proliferation and release of indigenous fish. The key results were as follows: The fish survey identified 15 species in Dianchi Lake, with only one being indigenous. The indigenous-to-exotic species ratio was 1:14 and the biomass proportion of indigenous fish was 6.4%. In the current biomass pyramid, small and medium-sized carnivorous fish accounted for only 0.07% of total fish biomass, significantly lower than the 1.8% of piscivorous fish at higher trophic levels. To optimize the trophic structure, we propose adjusting the biomass proportions of piscivorous, small-sized carnivorous, and omnivorous/herbivorous fish to 1%, 1.4%, and 76%, respectively, through the proliferation and release of indigenous species. Maintaining the total biomass of the ecosystem, the release of indigenous fish could enhance energy flow efficiency from 1.7% to 3.2%. Key ecological indices also improved: the ratio of total primary production to total respiration (TPP/TR) approached 1, the system omnivorous index (SOI) increased from 0.127 to 0.212, Finn’s Cycling Index (FCI) rose from 3.1% to 4.3%, and Shannon diversity index (H’) of fish increased from 1.599 to 1.649. These results suggest that the proliferation and release of indigenous fish can improve the community structure, enhance energy flow efficiency, and stabilize the ecosystem, thereby promoting the restoration of Dianchi Lake’s aquatic ecosystem.