Tropical cyclones are major episodic disturbances in coastal oceans, yet they produce contrasting ecosystem responses, ranging from abundance enhancement to biological suppression. This variability has limited efforts to predict how intensifying storms will alter coastal ecosystem dynamics. Here we combine two years of high-frequency in situ plankton imaging with atmospheric reanalysis, hydrographic observations and ocean circulation data to examine ecosystem responses across five typhoons in the northern South China Sea. Our observations suggest that storm intensity is associated with a shift in the balance between regional connectivity and local disturbance. Under weaker storms, ecosystem variability is primarily associated with horizontal water-mass exchange, as changing contributions of the Pearl River plume and offshore water reorganize plankton abundance. Under intermediate forcing, connectivity and disturbance interact, with strong plume influence partly offsetting the effects of enhanced mixing. Under the strongest storm, local disturbance dominates: mixed-layer deepening, sediment resuspension and elevated turbidity coincide with widespread zooplankton declines, largely independent of background water-mass conditions. Across events, turbidity emerges as the most consistent negative predictor of zooplankton abundance, linking physical disturbance to biological response. These results support a connectivity-disturbance framework in which storm intensity changes the dominant physical controls regulating coastal ecosystems, providing a mechanistic basis for interpreting divergent biological responses to tropical cyclones under a changing climate.