Simple Summary Ecological fishery management is one of the predominant approaches to lake ecological management in China; it involves the stocking of filter-feeding fish species to mitigate algal blooms. This strategy not only enhances water quality but also yields ecological benefits by fostering the growth of fish populations, thereby offering both ecological and economic advantages. Nonetheless, there is a scarcity of works in the literature addressing the effects on fish community dynamics and diversity in lakes subsequent to the cessation of ecological fishing practices. This study focuses on the initial changes observed in fish community composition and diversity following the cessation of an ecological fishery project in Qilu Lake, an eutrophic shallow lake situated in China. Ecological fishery projects aim to improve the water quality of eutrophication lakes by stocking filter-feeding fish species that feed on algae. The findings indicate a significant decline in the number of fish species, average individual size, and species diversity index following the cessation of fisheries-related activities (including fish stocking and fishing activities) due to the termination of the ecological fishery project in the lake. To preserve fish biodiversity and enhance water quality in Qilu Lake, it is recommended that policies be implemented to sustain the implementation of ecological fisheries projects, restore habitats for native fish species, and regulate the proliferation of small fish populations.Abstract The Qilu Lake is an eutrophic shallow lake located in Yunnan Province, China. An ecological fishery project was initiated in the lake from 2011 to 2021 to introduce filter-feeding fish species that feed on algae, with the aim of improving water quality. In January 2022, when the ecological fishery project expired, all fisheries-related activities (including fish stocking and fishing activities) ceased in the lake. To comprehensively evaluate the initial alterations in fish community structure and diversity resulting from the fishing cessation in the Qilu Lake, the present study conducted field surveys within the one year before the fishing cessation (referred to as BFC) and the one year after the fishing cessation (referred to as AFC). A total of twenty-one fish species were collected, including four native species. Four species were recorded in the lake for the first time, including Pelteobagrus fulvidraco, Pelteobagrus vachelli, Paramisgurnus dabryanus, and Hyporhamphus intermedius. The number of fish species decreased from 21 to 13 following the fishing cessation. The fishes collected in both BFC and AFC are mainly omnivorous-feeding and of bottom-dwelling habits. The mean size of the fishes in the AFC sample shows a significant decrease compared to those in BFC. After the fishing cessation, the Shannon-Wiener diversity index and Margalef richness index of the fish slightly declined. The fish community structure of the Qilu Lake exhibits a high degree of similarity to adjacent lakes in central Yunnan. Our study demonstrates a significant shift in the fish community of the Qilu Lake following the fishing cessation, one which may adversely impact the stability of the lake ecosystem. To enhance fish species diversity in the Qilu Lake, it is recommended that policies be implemented to promote the ecological fishery project and improve habitat restoration for native fish species, while also regulating fish community structure.