In order to understand the dynamic changes of community structure of zooplankton in ballast water, the experiment to mimic ballasting onboard was designed and carried out at land-based test facility. Samples were collected immediately after pumping finished (0 d) and then on days 1, 5, 10, 15, and 30 respectively. After 30d of holding, the abundance of zooplankton sharply decreased by 93.28% and the number of zooplankton taxa decreased from 11 to 5. During holding, the frequency and persistence of zooplankton were different.The adaptability of different taxa and species to each ballast stage was quite different. Nauplius larval and Copepodid larval mainly accounted for the a highest proportion at 5d, which was the main reason for the significant increase in zooplankton abundance.However, the decay rate did not reach 100% after the 30d holding. MDS analysis highlighted that zooplankton community in ballast water had drastic fluctuation. Canonical correspondence analysis (CCA) indicated that TN, TP and other nutrient conditions have a greater impact on zooplankton, followed by TSS and turbidity, and temperature.