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Although previous studies have recorded that tropical cyclones cause a significant increase in chlorophyll a concentration (Chl-a), most of these results were only based on surface Chl-a observed by satellite data. Using satellite, reanalysis and model data, this study investigated the response of the upper ocean and sea surface Chl-a to three different levels of tropical cyclones in the South China Sea. In our results, the severe tropical storm (STS) did not cause an increase in surface Chl-a or depth-integrated Chl-a in the short term (i.e., ~2 days); the typhoon (TY) increased the surface Chl-a from 0.12 mg·m−3 to 0.15 mg·m−3 in the short term, but the depth-integrated Chl-a did not increase significantly; the super typhoon (STY) caused the surface Chl-a to increase from 0.15 mg·m−3 to 0.37 mg·m−3 in the short term, and also increased the depth-integrated Chl-a from 40.41 mg·m−2 to 42.59 mg·m−2. These results suggest that the increase in the surface Chl-a after TY and STY were primarily caused by physical processes (e.g., vertical mixing). However, the increase in the depth-integrated Chl-a of STY may be due to the entrainment of both nutrients and phytoplankton through upwelling and turbulent mixing under the influence of STY.