Continuous input from the Changjiang River significantly reshuffled the ecosystems in the Changjiang Estuary and adjacent East China Sea, impacting the production, distribution, and emission of marine dimethyl sulfide (DMS). However, the effect of phytoplankton biomass and composition on DMS under different nutrient inputs remains poorly understood. Two comprehensive cruises to characterize their effects were conducted in spring and summer 2015. The areas with high concentrations of DMS, dimethylsulfoniopropionate (precursor of DMS), and dimethyl sulfoxide (photo‐oxidation product of DMS) were largely consistent with high phytoplankton abundances along the front of Changjiang Diluted Water in both seasons. Both the higher conversion ratio of dissolved dimethylsulfoniopropionate to DMS and the higher DMS biological production rate in summer contributed to the higher DMS levels. Once produced in seawater, more than half of the DMS was directly consumed by microbes, resulting in a turnover time of 1–2 days, which was shorter than that driven by ventilation. A ship‐based incubation experiment revealed that, with increasing N/Si and N/P ratios from the Changjiang River, phytoplankton biomass increased and the community shifted from diatom‐dominated to dinoflagellate‐dominated, which was conducive to DMS production. It was noteworthy that strong DMS photo‐degradation induced by high nitrate concentrations may have masked DMS production to some extent, while urea only had a promoting effect and therefore led to a maximum increase in DMS yield. Our findings indicated that the increase in phytoplankton biomass and succession of phytoplankton community induced by changes in nutrient inputs will promote DMS emissions from the Changjiang Estuary.