The climate and surface currents of the northeastern Indian Ocean are controlled by the Indian Monsoon, and its marine primary productivity is the foundation of the ecosystem, which connects the atmosphere and ocean carbon cycle. In this study, coccolith quantitative analysis has been carried out from the marine sediments in Core I105A on the 90°E Ridge of the northeastern Indian Ocean to obtain the records of the coccolith absolute abundance and the relative percentages of dominated coccolithophore species, which are used to reconstruct the variation of marine primary productivity in thenortheastern Indian Ocean since last glaciation. The results show that the marine primary productivity in this area has experienced through three stages since last 54 ka: (1) high productivity during the last glaciation; (2) a significantly decrease in productivity during the deglaciation; and (3) the lowest productivity during the Holocene. This kind of pattern is basically consistent with the variations of other paleo-productivity proxies in the Bay of Bengal. Comparison with the paleoenvironmental data of the Indian Ocean indicates that the marine primary productivity decreases when the freshwater input to the northeastern Indian Ocean increases due to intensified Indian Summer Monsoon. It reveals that the evolution of marine primary productivity in the northeastern Indian Ocean since the last glaciation has most probably been driven by seawater stratification associated with the precipitation of the Indian Summer Monsoon, a process regulated by the Earth orbital precession cycles.