Phytoplankton is the most important primary producer in aquatic ecosystems and acts as the base of the biological pump, understanding their diversity and productivity is of great scientific significance for the study of ocean carbon flux. As a typical "blue carbon" ecosystem, the first mangrove National Nature Reserve, Dongzhai Harbor, is an ideal site to explore the carbon burial capacity of the coastal zone, but there were limited studies on phytoplankton diversity in Dongzhai Harbor, especially on the assessment of carbon fixation potential. In this study, we take the mangrove protection aquatic area of Dongzhai Harbor in Hainan Island as the research site to explore the phytoplankton community structure, diversity, carbon fixation, and related environmental influencing factors in the dry and wet seasons. Since the potential environmental factors will vary with seasons and space, the associated phytoplankton community structure is supposed to change. We mainly emphasize the contribution of the phytoplankton community to primary productivity and then evaluate the carbon sequestration potential of phytoplankton. Different phytoplankton groups had differential contributions to primary productivity in the wet and dry seasons. Physicochemical parameters (e.g. dissolved oxygen, salinity, etc.) affect phytoplankton community composition and primary productivity, thus affecting the assessment of phytoplankton carbon sequestration potential.