Abstract The Taiwan Strait, located between Taiwan Island and the southeast of the mainland of China, is the main passageway connecting the East China Sea and the South China Sea. The particular coastline of the mainland created several semi-enclosed embayments along the west coast of the Taiwan Strait. Runoffs from land bring large amounts of nutrients into the bays, which made these bays important natural spawning and breeding grounds for several economically important marine organisms. In order to reveal the effects of the China Coastal Current (CCC) on the zooplankton communities in Fuqing Bay in northeastern Fujian, zooplankton samples were collected at 12 stations in early March 2014. The average surface seawater temperature was 12.53 ± 0.14°C, and salinity was 28.33 ± 0.21 PSU in the investigation area during the research period. In total, 23 identified copepod species and in addition several unidentified benthic harpacticoid copepods were recorded with an average abundance of 77.44 ± 60.07 ind. m−3. In the present study, the most dominant group consisted of juveniles (copepodites) with an average density of 59.97 ± 51.49 ind. m−3, which was followed by Calanus sinicus Brodsky, 1965 with an average density of 5.04 ± 4.95 ind. m−3. The occurrence rate of Calanus sinicus was 91.67% in our study, which indicates that the research area was controlled by the CCC water mass. So, we concluded that the CCC played an important role in transporting cold water copepod species from the Bohai Sea and the Yellow Sea to the western Taiwan Strait. A noteworthy discovery in our samples was Eurytemora pacifica Sato, 1913, which was recorded for the first time in waters of the western Taiwan Strait with an occurrence rate of 33.33% and an average density of 0.81 ± 1.91 ind. m−3. Eurytemora pacifica was first reported at Yantai harbour and is widely distributed in waters of the northern Pacific Ocean. The co-occurrence of Calanus sinicus and Eurytemora pacifica in our research area possibly indicates that E. pacifica could be used as a bioindicator for the directional movement of the CCC. The high occurrence of this species in our research area indicated that the CCC affects the community structure of copepods in the western Taiwan Strait in early spring.