Zooplankton, as a secondary producer, play an important role in marine food webs and biogeochemical cycles. Due to their small size, fast metabolism and floating lifestyle, zooplankton can respond quickly to the variability in marine environments and can indicate effectively the changing ocean. Based on a review of the scientific investigation of zooplankton in the South China Sea, this paper summarizes the current status of zooplankton species diversity in the South China Sea, and compares and analyzes the distribution of zooplankton communities in the typical ecological environments (Pearl River Estuary, Daya Bay and coral reefs) and the continental shelf, slope and basin in the northern and southern waters of the South China Sea at both horizontal and vertical scales. The effects of monsoon, monsoon-driven ocean currents, water masses and habitat heterogeneity on zooplankton community structure were discussed. Combined with the hot spots and difficulties in zooplankton research under the background of climate change and human activities, the shortcomings of zooplankton research in the South China Sea were pointed out, and the research prospects in biodiversity, ecological functions and biological oceanography were proposed. It is expected to provide a basic basis for biodiversity conservation, biogeochemical cycles and sustainable utilization of marine resources, as well as scientific support for the adaptability of the marine ecosystem to climate change in the South China Sea.