The Pearl River Estuary and adjacent seas in South China Sea are frequently affected by tropical cyclones (TCs). Previous in situ and remote sensing studies have found that typhoons can enhance phytoplankton biomass and induce blooms in this region. However, the mechanistic links between phytoplankton blooms and typhoons have not been well understood due to the interplay of multiple complex processes along the land‐ocean‐atmosphere interface. Here, we constructed an integrated modeling system with the marine ecosystem and sediment components for the China Great Bay Area. By using the integrated modeling system, we quantitatively investigated the phytoplankton response to hydrological conditions variations under Typhoon Hato (2017), a strong typhoon case. Passive tracer experiments showed that with high river discharge induced by heavy rainfall, the residence time within Lingding Bay is as short as 15 days, less than half of that under the climatological discharge. The increase in freshwater pulse washes out the phytoplankton biomass within Lingding Bay. While for the offshore region, the analysis of various source and sink terms for the offshore region's post‐typhoon response showed that the increase of phytoplankton biomass in the first week was because of the uplift of nutrient‐rich subsurface water, while in the second week, it was due to the seaward propagation of nearshore high phytoplankton biomass water. While riverine nutrients support phytoplankton growth in the third week, a large part of phytoplankton biomass was lost to zooplankton grazing, showing the system shifted from the bottom‐up control to the top‐down control.