The withdrawal of aquaculture facilities has an important impact on the aquatic ecosystem of the lakes connected to the Yangtze River. In order to elucidate the response mechanism of metazooplankton to the changes in water environment after the removal of aquaculture facilities, we collected metazooplankton samples and investigated the water environment in the Huayanghe Lakes from the summer of 2018 to the spring of 2019. Aquatic plants recovered quickly, and water eutrophication was relieved, especially in Lake Huangda, followed by Lake Bo. During our study, the highest regional (γ) diversity was 71 in summer, while the lowest was 32 in winter. Species turnover in space (β diversity) varied between 10.01 and 56.52, which was highest in summer. Based on redundancy analysis, environmental factors such as transparency, Chl α, water temperature and water depth, had greatly effects on the metazooplankton community structure. The results showed that the restoration of aquatic plants increased species diversity and metazooplankton density. This study provides a data basis for lakes restoration and a scientific basis for the management and protection of lakes water ecosystem.