Under eutrophication background, the increasing dinoflagellates blooms relative to diatoms blooms off the Changjiang Estuary has caused much concern. Changes in the composition of the phytoplankton community can affect the burial of organic matter and the accumulation of recalcitrant dissolved organic carbon, which in turn affects the overall carbon uptake capacity of the ocean. This study adopted a combination of DOC, DON and ultrahigh-resolution mass spectrometry to study the differences in the composition of DOM released from the degradation of diatoms and dinoflagellates and the stability of these DOM through incubation. Furthermore, the impacts of diatom and dinoflagellate succession on DOM pools in the Changjiang estuary and its adjacent area were discussed based on the changes in DOM composition and distribution in different seasons (after impacts of different algal blooms).