Abstract: Zooplankton serves as a key component of marine ecosystems, playing critical roles in fisheries resources and carbon sequestration. Mesoscale eddies can significantly influence the community structure and functional traits of zooplankton by modulating hydrological conditions and biogeochemical processes. To investigate the influence of mesoscale eddies on the vertical distribution of zooplankton, this study systematically analyzed the community composition, size structure, and regulatory mechanisms in cold eddies (CEs), warm eddies (WEs), and background regions of the central South China Sea by using vertically stratified (0~700m) samples collected with a MultiNet system in September 2024 combined with concurrent environmental data. A total of 440 zooplankton species were identified, belonging to 12 taxonomic groups. Copepoda were the predominant group (254 species, 57.73%), followed by ostracoda (34 species), jellyfish (32 species), and shrimp (26 species). The species richness and abundance of zooplankton all exhibited distinct vertical stratification, with maximum values concentrated in the upper 100m layer and decreasing with depth. Mesoscale eddies significantly shaped the distribution patterns: CEs enhanced total abundance and biomass, with increased relative biovolume of larger individuals in deeper layers. In contrast, WEs reduced copepod dominance and shifted the community toward smaller sizes. Cluster analysis revealed that the zooplankton community in the 0~700m layer could be delineated into three typical vertical assemblages: the surface community (0~100m) was dominated by species such as Calocalanus styliremis and Oithona plumifera; the mid-water community (100~400m) was characterized by the dominance of Pleuromamma gracilis and Lucicutia flavicornis; and the deep community (400~700m) was notably dominated by Metridia brevicauda, Triconia conifera, and Oncaea gracilis. Normalized biomass size spectrum (NBSS) analysis revealed that the NBSS slope flattened and the intercept declined with depth. CEs region flattened the NBSS slope and raised the intercept, indicating higher productivity and energy transfer efficiency, whereas the WEs region exhibited an opposite trend. This pattern indicates higher zooplankton productivity and energy transfer efficiency in the CEs. The influence of environmental factors were depth-dependent: the layer above 200m was primarily influenced by temperature, dissolved oxygen, salinity, and chlorophyll-a, whereas the layer below 200m was mainly governed by temperature and dissolved oxygen. This study elucidates how mesoscale eddies influence the vertical distribution, size structure, and transfer efficiency of zooplankton by altering water column properties and nutrient regimes, thereby providing a scientific basis for enhancing the understanding of carbon cycling and energy flow in the central South China Sea.

Key words: Zooplankton, Vertical distribution, Mesoscale eddy, Size structure, South China Sea