The strong western Pacific boundary current of the Kuroshio significantly affects the oceanographic and ecological processes of the East China Sea through its branches. To understand the seasonal variation of Kuroshio intrusion and its ecological effects, 10 cruises were conducted from February 2015 to January 2016 in the waters adjacent to the Changjiang River estuary to collect hydrological data and abundances of phytoplankton assemblages of Prochlorococcus (Pro), Synechococcus (Syn) and picoeukaryotes. High salinity bottom water representing the Nearshore Kuroshio Branch Current (NKBC) appeared in the spring, peaked in the summer, and then almost disappeared at the end of the autumn. During this period, the seasonal variations of Pro and Syn subgroup with lower orange fluorescence (dim type Syn) abundances correlated and synchronized with the intensity of the NKBC intrusion. Water masses analysis further illustrated that the spring was the critical season for NKBC to influence and transport phytoplankton along the pathway to coastal waters. NKBC will further impact the phytoplankton dynamics and ecological processes in this sea area.