Suzhou Industrial Park is located in the lower reaches of the Yangtze River Basin. With the continuous progress of urbanization, the stability of structure and function of the aquatic ecosystem in the Park is facing severe challenges. Zooplankton, as an important part of the aquatic ecosystem, is of great significance for the biodiversity protection and healthy development of the ecosystem by researching the formation mechanism of its community structure. Moreover, zooplankton is very sensitive to environmental changes, and the water pollution status can be evaluated based on its community structure characteristics. To better understand the community structure and influencing factors of metazoan zooplankton in five lakes of Suzhou Industrial Park, four surveys were conducted from July 2018 to June 2019. At the same time, five physical and chemical factors of water body, lake area, and the closest distance from samples to the shore were measured. A total of 112 metazoan zooplankton species (including 65 species of Rotifera, 29 species of Cladocera, and 18 species of Copepoda) were detected in this study, in which 12 species were dominant species (including 10 species of Rotifera, 1 species of Cladocera, and 1 species of Copepoda). Jaccard similarity analysis indicated that the species compositions of metazoan zooplankton among lakes were moderately similar. The density of metazoan zooplankton showed the significant differences in different seasons and locations, while biomass, Shannon-Wiener diversity, Pielou evenness, and Margalef richness indexes only had significant differences in seasonal aspect. The results of cluster analysis suggested that the metazoan zooplankton community structure was the most similar in summer and autumn. It was revealed that temperature, dissolved oxygen, and pH were the main environmental factors affecting the community structure of metazoan zooplankton by redundancy analysis. Pearson correlation analysis indicated that there was no significant correlation between lake area and metazoan zooplankton community structure, while a significantly positive correlation between the distance from samples to the shore and metazoan zooplankton biomass was detected. Based on the water quality evaluation standard and species diversity indexes, the water quality of the lakes in the Park was at a light to moderate pollution level. Overall, the metazoan zooplankton community structure in the five lakes of Suzhou Industrial Park showed a trend of homogeneity, and the seasonal variation, environmental factors and the distance from samples to the shore were main factors regulating the formation of community structure. The results of metazoan zooplankton community structure could provide an effective reference for the restoration and development of lake water in the Park.