The variability of chlorophyll a concentration (Chl a) in the open South China Sea (SCS) was examined using observations from two Bio‐Argo floats. During the period of September 2014 to August 2015, there was a permanent subsurface Chl a maximum (SCM) in the depth range of 48 to 96 m in the central basin of the SCS. In the northern basin, the SCM disappeared in winter, replaced by enhanced surface layer phytoplankton with high Chl a. The values of the SCM were influenced by the vertical displacement of isotherms. Strong wind forcing and surface cooling were the main physical drivers of high surface Chl a in winter. In the north, stronger wind than in the center, lower sea surface temperature (SST) than in the center, and Kuroshio water intrusion were more favorable for the upward transport of nutrient‐rich deep water. A large amount of nitrate could be advected from the Taiwan Strait and shallow continental shelf to the northern basin in winter. A combination of strong wind mixing, surface cooling, Kuroshio water intrusion, and horizontal advection caused the winter surface phytoplankton bloom in the north.