Protozooplankton regulate microbial food webs through top-down control and nutrient cycling, yet their grazing impacst under ocean warming, particularly in subsurface chlorophyll maximum (SCM) layers, remain poorly understood. This study investigated spatial and seasonal variability in protozooplankton grazing in the northern East China Sea, influenced by Tsushima Warm Current (TWC) intrusion and stratification. Thirty in situ dilution experiments were conducted in surface and SCM layers to quantify grazing impacts on dominant diatoms and dinoflagellates across natural temperature gradients. Light limitation was excluded (Zm/Zeu<1), and nutrients were enriched to isolate temperature effects. Grazing impact increased with temperature up to 29°C at the surface and 27°C in the SCM, indicating intensified top-down control even during extreme heat events. Grazing pressure was generally lower on bloom-forming species and in coastal waters, facilitating bloom development. In the SCM layer, elevated grazing rates coincided with high phytoplankton growth under conditions of moderate light availability and nutrient-replete conditions, suggesting rapid turnover and strong trophic interactions. Higher carbon biomass of ciliates and mixotrophic dinoflagellates in the SCM layer also indicated active grazing and nutrient competition with phytoplankton, supported by the lack of significant differences in growth rates between nutrient–enriched and depleted treatments. These findings reveal that warming-driven shifts in protozooplankton grazing and mixotroph-phytoplankton interactions may reshape bloom dynamics and nutrient flows in stratified marine ecosystems. This study highlights the critical role of top-down processes in regulating phytoplankton blooms and provides insights into microbial food web responses under future ocean warming scenarios.