Marine heatwaves (MHWs) are increasingly recognized as abrupt drivers of coastal ecological change, but their impacts on ecosystems are often simplified to thermal stress and one-dimensional vertical stratification that limits nutrient supply. This vertical framework overlooks critical horizontal processes in river-influenced shelf ecosystems, where MHWs interact with plume dynamics and cross-shelf gradients. Here, we investigate a strong June 2019 MHW in the northern South China Sea, combining in situ shipboard observations during the event, historical summertime measurements, and complementary satellite remote sensing and reanalysis datasets for baseline comparison, to characterize its multifaceted physical and ecological impacts. The MHW was driven by anomalously weak winds, which also triggered southeastward plume expansion and intensified upper-ocean stratification. Phytoplankton responses diverged sharply across the shelf: in plume-influenced inshore waters, nitrate and total chlorophyll-a increased significantly, with elevated dinoflagellates, haptophytes, and Synechococcus. In plume-limited offshore waters, diatoms declined and Synechococcus increased, indicating community miniaturization. These contrasting patterns reveal that MHWs amplify pre-existing cross-shelf contrasts via coupled hydrographic and nutrient reorganization, rather than acting through thermal forcing alone. Our study highlights the importance of compound event frameworks for understanding MHW impacts in heterogeneous coastal systems and improves predictive capacity under climate change.