The variability of phytoplankton biomass related to ocean’s biological carbon pump in the central tropical Indian Ocean (CIO) is not fully understood. Using satellite and BGC-Argo data, we found that phytoplankton biomass exhibits significantly different and even opposite changes at the near-surface (0-10 m) and subsurface layer (50-100 m). Results showed that the shoaling/deepening of the mixed layer and thermocline dominated the phytoplankton biomass change in different layers. In February-May, the shallow MLD exacerbated the oligotrophic environment in the mixed layer, thus resulting in low near-surface phytoplankton biomass (Chl a <0.1 mg m^-3). However, strengthened wind stress and surface cooling induced deep vertical mixing (MLD > 50 m), hence increasing the supply of both nutrients and phytoplankton from the subsurface to maintain the near-surface phytoplankton blooms (Chl a > 0.2 mg m^-3) in June-October. Below the mixed layer, wind-induced upwelling/downwelling modulated the thermocline, which significantly affects the supply of nutrients for phytoplankton growth in the subsurface layer. The shallower thermocline during February-March provided favorable conditions for the subsurface blooms (Chl a >0.5 mg m^-3) with a prominent subsurface chlorophyll maximum layer (SCML). Conversely, the deeper thermocline in June-July was related to the lowest phytoplankton biomass with the disappearance of the SCML. These results may help explain the response of vertical phytoplankton to changes driven by multiple atmospheric and physical forcing factors in future climate-change scenarios.