A phytoplankton bloom was observed in the southeastern Arabian Sea after the passage of the anti-S-type track Tropical cyclone ARB 06 in 1998, which lasted for 22 days. The dynamic mechanism of the phytoplankton bloom was investigated with high-resolution satellite remote sensing data, reanalysis data and buoy data. The results show that the double thermocline structure hindered the uplift of deep nutrients to the surface before the tropical cyclone arrival. During and after the passage of the cyclone, the shallower thermocline disappeared, the deeper thermocline changed from 45.7 m to 76.5 m, the mixed layer deepened, and the upper oceanic stratification weakened. Additionally, a weak ocean eddy pair was enhanced gradually after the passage of cyclone. The relative vorticity of the ocean eddy pair was calculated. In the oscillation with a period of two days, the vorticity of the cyclonic eddy was stronger than that of the anticyclonic eddy, which enhanced a strong upwelling at a depth of more than 55 m for more than 10 days. The vertical current shear generated by the oscillation not only enhanced the vertical mixing, but also plays an important role in the distribution of phytoplankton blooms. The phytoplankton bloom was triggered by the nutrient below the thermocline into the sea surface, where a strong upwelling and weakened oceanic stratification occurred after the passage of cyclone. This study offers new insights on the mechanism of phytoplankton bloom induced by tropical cyclones and will be helpful for evaluating tropical cyclone-induced biological responses in future.