To mitigate the decline of fishery resources and the exacerbation of water pollution in Chinese lakes and to enhance the potential and sustainable use of lake fisheries, the Chinese government has actively implemented principles and models of ecosystem-based lake fishery management. This includes promoting ecological aquaculture techniques and the âretiring pens to restore lakesâ policy. To assess the effects of ecosystem-based management on Chinese lake fisheries, data from 2007 to 2020 were collected for the Qiandao Lake, Tai Lake, Hongze Lake, Luoma Lake, and Gaobao Lake in the middle and lower reaches of the Yangtze River. The study employed Data Envelopment Analysis (DEA) to assess fishing efficiency through a static input-output efficiency model. Additionally, the Malmquist index and distance functions were used for a dynamic comparison of total factor productivity (TFP) across the five lake management models. The results indicate that trends in technological progress, scale efficiency, and TFP were consistent across the lakes from 2013 to 2020. Qiandao Lake, Tai Lake, and Hongze Lake showed a positive average annual growth rate in TFP, with Qiandao Lake having the highest average annual growth rate of 13.2%. In contrast, Gaobao and Luoma Lakes experienced a negative growth rate in TFP. Furthermore, Qiandao Lake exhibited significantly higher technical efficiency than the other four lakes, effectively achieving an efficient state, followed by Hongze Lake. The study demonstrates that technological progress and variations in scale efficiency are the primary factors driving the increase in TFP in fisheries. Promoting ecosystem-based âfishing for water conservationâ aquaculture techniques and restricting aquaculture scale through the âretiring pens to restore lakesâ policy contribute to enhancing TFP in ecological fisheries.