The northern Indian Ocean is globally significant for its seasonally reversing winds, upwelled nutrients, high biological production, and expanding oxygen minimum zones. The region acts as sink and source for atmospheric CO2. However, the efficiency of the biological carbon pump to sequester atmospheric CO2 and export particulate organic carbon from the surface is not well known. To quantify the upper ocean carbon export flux and to estimate the efficiency of biological carbon pump in the Bay of Bengal and the Indian Ocean, seawater profiles of total 234Th were measured from surface to 300 m depth at 13 stations from 19.9°N to 25.3°S in a transect along 87°E, during spring intermonsoon period (March–April 2014). Results showed enhanced in situ primary production in the equatorial Indian Ocean and the central Bay of Bengal and varied from 13.2 to 173.8 mmol C m−2 d−1. POC export flux in this region varied from 0 to 7.7 mmol C m−2 d−1. Though high carbon export flux was found in the equatorial region, remineralization of organic carbon in the surface and subsurface waters considerably reduced organic carbon export in the Bay of Bengal. Annually recurring anticyclonic eddies enhanced organic carbon utilization and heterotrophy. Oxygen minimum zone developed due to stratification and poor ventilation was intensified by subsurface remineralization. 234Th‐based carbon export fluxes were not comparable with empirical statistical model estimates based on primary production and temperature. Region‐specific refinement of model parameters is required to accurately predict POC export fluxes.