Based on both physical and biological data collected from multi-source satellite during summer typhoon Linfa, we found that the typhoon triggered two phytoplankton declines and three phytoplankton blooms in the northern South China Sea (SCS), where the waters were influenced by coastal upwelling and the input of terrigenous materials from the Pearl River estuary (PRE). One phytoplankton decline (about a 3-fold reduction) in the continental shelf region can probably be attribute to the limited nutrient supply induced by the decayed coastal northeastern current and onshore Ekman transport (OET) and Kuroshio intrusion water, as well as the uplifted subsurface’s low chlorophyll-a (Chl-a) concentration driven by vertical mixing and upwelling. Another phytoplankton decline (about a 3.5-fold reduction) in the eastern Leizhou Peninsula-coastal upwelling region is probably caused by OET and a decayed coastal northern current. Conversely, the decayed coastal current, OET, and the vertical mixing and upwelling could lead to the transport of nutrient-rich water from the PRE to the nearshore region of the southwestern PRE mouth, and from the subsurface layer to the surface, respectively, thereby stimulating the growth of phytoplankton in the nearshore region (increased by about 4-fold) and the open ocean (increased by about 2.3-fold). In the Shantou (the coastal upwelling region), the phytoplankton responses to nutrient supply were feeble when phytoplankton was already growing in nutrient replete conditions. In addition, the OET and the high turbidity barely resulted in moderate phytoplankton bloom (increased by 38%). In summary, the physical driving forces associated with typhoons that modulates phytoplankton dynamics are the nutrient and phytoplankton transportation in the northern SCS during the wet season.