Marine heatwaves (MHWs) have become increasingly frequent under climate change and can substantially affect coastal ecosystem. However, the ecological responses of shallow coastal seas to both warming and cooling temperature extremes remain poorly understood. In this study, a coupled physical–biogeochemical model (FVCOM–ICM) was used to investigate summer (June, July, and August) MHW characteristics in the Bohai Sea during 2010–2019 and to quantify phytoplankton responses to sea surface temperature (SST) extremes. MHWs exhibited distinct spatial distribution in the Bohai Sea, with higher frequency, longer duration, and stronger intensity occurring in nearshore regions within the 10-m isobath. The mean maximum intensity across the Bohai Sea was 1.36 °C, while the highest bay-scale averaged maximum intensities within the 10-m isobath reached 2.01 °C in Laizhou Bay, 2.78 °C in Bohai Bay, and 2.76 °C in Liaodong Bay. Based on these observed MHW characteristics, SST perturbation experiments of ±1.5 °C and ±3.0 °C were conducted for the summer of 2017 to represent both typical and extreme temperature anomalies in the Bohai Sea. Results showed that SST cooling generally enhanced phytoplankton biomass and reduced dissolved inorganic nitrogen (DIN) concentrations. As SST approached the optimal growth range for phytoplankton, gross primary production increased while respiration remained relatively low. Consequently, nutrient uptake increased, resulting in higher phytoplankton biomass. In contrast, SST warming increased respiration and suppressed phytoplankton growth once temperatures exceeded the optimal range. As a result, phytoplankton biomass declined, accompanied by weaker DIN accumulation. Grazing and algal settling responded consistently with changes in phytoplankton biomass. By modifying SST only within the ecological module while maintaining identical hydrodynamic conditions, this study isolated the direct thermodynamic effects of temperature anomalies on ecosystem processes. These findings improve our understanding of how warming and cooling extremes regulate nutrient and phytoplankton dynamics in shallow coastal seas and provide insights into ecosystem responses under future climate change.