It is very important to monitor and protect the water environment and biological resources in Baiyangdian Lake because of Xiong’an New Area. In order to investigate the spatial and temporal variation characteristics of the community structure of Cladocera and Copepods and their relationship with water environmental factors in Baiyangdian Lake, canonical correlation analysis (CCA) was used to analyze the abundance, diversity index and aquatic environmental factors of Cladocera and Copepods in Baiyangdian measured in May, August and October 2019. Based on the technology of DNA barcoding, 26 species of Cladocera and Copepods were identified belonging to 8 families, 17 genera. The dominant species are Bosmina coregoni, Thermocyclops hvalinus and Ectocyclops phaleratus throughout the year 2019. The spatial and temporal characteristics of abundance and diversity index are different. The main expression is that the variation of regional distribution is greater than the seasonal variation, and it is greater in the southern region than in the northern region in space. Analysis of correlation between Cladocera and Copepods community structure and water environment, the results showed that temperature, transparency, nutrients and other environmental factors affected the growth, development, feeding and other activities of Cladocera and Copepods as the main environmental factors affecting their abundance and community structure characteristics. S, Pb and Zn are the key influencing factors, which have significant negative effects on Cladocera and Copepods. Therefore, the long-term ecological environment monitoring and species research in Baiyangdian Lake will provide reference for the implementation of water conservancy projects and construction of Xiong’an New Area.