As a marginal sea, the South China Sea (SCS) is generally deemed oligotrophic. Nevertheless, winter blooms were frequently observed to the west of the Luzon Strait. In contrast with the relatively clear seasonal dynamics, the governing factors of the blooms have rarely been elaborated, especially on the synoptical scale. To investigate the dynamics underlying the blooms, we developed a process-oriented submesoscale-permitting physical-biological coupled model, simulating the Bio-Argo observed winter bloom event in 2014-2015. Seasonally, the chlorophyll maximum existed in the subsurface (~ 50 m) during summer and autumn, while in winter the wind-induced mixing and upwelled nutrients prompted the phytoplankton to flourish in the surface layer (0 ~ 50 m). On the synoptical scale, occasional blooms happened under the joint influence of mesoscale and submesoscale processes. Through modeling diagnosis, we demonstrated that the mesoscale processes induced the upwelling through advection of vorticity. Submesoscale baroclinic instabilities affected the phytoplankton growth in the surface layer with enhanced light exposure by restratification. Under the impact of submesoscale processes, the initiation of the winter bloom was advanced in the northern SCS.