The coastal current, cyclonic eddy, and coastal upwelling are monsoon-driven ubiquitous physical processes operating along the continental shelf of the northwestern South China Sea (NWSCS). To explore their influence on the copepod community structure, zooplankton specimens were sampled in the NWSCS in the summer and winter of 2006. A total of 159 copepod species were identified from 50 genera, 25 families, and four orders. The number of species in summer was significantly higher than that in winter (t-test, t = 6.025, p < 0.001). Furthermore, offshore samples tended to have a greater number of species than nearshore samples in the two seasons. In summer, copepods were concentrated in the waters off the cyclonic eddy and its adjacent waters, with a maximum abundance of 528 ind.m⁻³, and in winter they were mainly concentrated along the coastal waters. Among 13 dominant species in total, Canthocalanus pauper and Subeucalanus subtenuis were the most common species in summer and winter, whereas Calanus sinicus only occurred in summer. Redundancy analysis and Pearson correlation analysis showed that temperature, salinity, dissolved oxygen, and chlorophyll a concentrations were important environmental factors affecting the copepod community structure. In addition, monsoon-driven ocean currents exhibited direct impacts on the migration of copepods, and indirect regulation of their horizontal distribution and seasonal patterns by changing the hydrological environment. Calanus sinicus was a reliable indicator of coastal currents and the cyclonic eddy, while Paraeuchaeta russelli was a good indicator of the coastal upwelling.