It has been reported that community structure of crustacean zooplankton is related to environment factors and abundance of predacious fishes. Most studies, however were based on observation on independent water bodies, which may complicate the results with uninterested factors. A large river-connected lake has partitioned regions with the characteristics of either a river or a lake albeit allowing exchanging of zooplankton of different regions. Thus, a river-connected lake is an ideal system for studying distribution of crustacean zooplankton and investigating its affecting factors. In this study, 11 stations of a large river-connected lake, Lake Gaoyou, were sampled in all four seasons. Taxonomic diversity and species abundance were recorded and their correlation with environmental factors was investigated. A total of 26 and 22 species of crustacean zooplankton were recorded in the river and lake region, respectively. The abundance of crustacean in the river region was significantly higher than that in the lake region. The relative abundance of calanoids and Bosmina fatalis in the river region was lower than that in the lake region, whereas the abundance of cyclopoids and other cladocera species was lower in the lake region than in the river region. Cluster analysis showed that crustacean assemblages could be divided into two, one cluster grouping all sites from the river region, and the other cluster included all sites in the lake region. According to Pearson correlation and canonical correspondence analysis, the distribution of crustacean was positively correlated with water temperature and chlorophyll a gradient. Chlorophyll a and fish abundance are excellent predictors on spatial distribution of crustacean zooplankton in Lake Gaoyou. Our findings may also help in planning of bighead carp stocking in Lake Gaoyou.