The northern East China Sea is one of the Large Marine Ecosystems, which experiences the fastest ocean warming across the globe. With the anticipation of stimulated Tsushima Warm Current (TWC) transport and rapid ocean warming, the importance of picoplankton will increase in this ecosystem. Thus, the spatiotemporal distribution of picoplankton was investigated in the northern East China Sea, where variability of TWC can modulate temperature and stratification. High contributions of warm and less saline Tsushima Surface Warm Water (TSWW) increased water temperature and stratification. Picoplankton were responsible for 75% of the relative contribution of chl a. PicoC:PicoChla ratios increased with distance from the coasts and fluctuated with depth, indicating that an elevated contribution of Tsushima Warm Water diminished the photosynthetic activity of picoplankton. Synechococcus I population decreased with salinity. High contribution of TSWW increased Prochlorococcus and Synechococcus II population, related with stratification and rising temperature driven by TSWW, respectively. Picoplankton‐derived carbon contents were mostly attributed either to picoeukaryotes or to Synechococcus depending on the TSWW contribution. This suggests that the rising TSWW contribution can intensify the role of Synechococcus in picoplankton‐derived organic matter in the northern East China Sea.