Satellite ocean color imagery indicates that typhoons enhance sea surface chlorophyll concentrations along their paths. However, the influence of typhoons on microphytoplankton community dynamics is still poorly understood because of the risk of sampling at sea under extreme weather conditions. From 22 July to 26 August, 2009, before and after the passage of the devastating Typhoon Morakot (7–9 August), 7 field cruises were conducted at a station in the southern East China Sea, northeast of Taiwan. Microphytoplankton species composition and related hydrographic and nutrient samples were analyzed. The diatom abundance increased by approximately 50 times just 10 d after the passage of Morakot, and the diatom population was dominated by chain-forming centric diatoms (Chaetoceros spp.) instead of the Trichodesmium and Gymnodinium spp. that prevailed before the typhoon. The strong winds and heavy rains of Morakot caused nutrient entrainment from upwelling and nutrient-enriched floodwaters with a low N:P ratio, driving the observed diatom bloom and change in species composition. The diatom bloom was terminated within 24 h. Based on the concurrent increase in copepods, we suggest that intensive grazing pressure was the main cause of the termination of the diatom bloom induced by Typhoon Morakot.