The Indian Ocean Dipole (IOD) is the predominant interannual climate mode and is critical in regulating the biogeochemical cycles of the equatorial Indian Ocean (EIO). However, the dynamics of nutrient supply and the magnitude of biological responses are less understood. Here, by comparing the biophysical in situ observations across the eastern EIO during the decaying period of a positive IOD in 2019 and neutral condition in 2017, we identify that the shoaling thermocline, initiated by reinforced easterly wind, lifts the nutricline into the euphotic layer under positive IOD condition. Coincidently, the strong turbulent mixing induced by the shear instability between the opposite‐flowing surface current and subsurface Equatorial Undercurrent increases the upward turbulent nutrient flux into the euphotic zone. Their combined effect triggers a vigorous subsurface biological response over the eastern EIO, with approximately twofold higher integrated chlorophyll‐a contents in the water column during a positive IOD than under neutral condition. Plain Language Summary: The availability of nutrients in the sunlit layer is the main factor limiting microalgae growth, which is the primary producer of marine ecosystems. Particularly in the tropical oceans, strong stratification due to warm and less salty surface water inhibits nutrient replenishment from the deep layer, leading to weak seasonality in primary production. With the occurrence of climate variability, for example, the Indian Ocean Dipole (IOD), an ocean‐atmosphere coupled climatic phenomenon, can significantly impact the biogeochemistry and ecosystem in the equatorial Indian Ocean (EIO). However, high‐resolution in situ observations, which can reveal the mechanism of nutrient supply and biological response under IOD conditions, are still lacking. We show that the combined effect of thermocline shoaling and subsurface turbulent mixing triggered an apparently elevated nutrient supply and a subsequent robust subsurface biological response in the eastern EIO during the decaying period of an extreme positive IOD in 2019. This study may aid in understanding the evolution of marine ecosystems during the greenhouse warming era. Key Points: A biological subsurface eastern equatorial Indian Ocean was observed during decaying period in a positive Indian Ocean Dipole (pIOD)The shoaling thermocline driven by reinforced easterly wind lift the nutricline into the euphotic layer in the pIOD phaseIncreased turbulent nutrient flux is caused by vertical shear due to the opposite‐flowing surface current and Equatorial Undercurrent [ABSTRACT FROM AUTHOR]