Abstract: The study on the analysis of pollution sources in the basin and the clarification of pollutants sources, fluxes into the sea and spatial distribution pattern of pollutants can provide basic information support for the formulation of marine ecological environment protection planning and the implementation of precise emission reduction measures. Pollutant export coefficient model and retention model were integrated to evaluate total nitrogen (TN) and total phosphorus (TP) fluxes into the sea and analyze the sources of pollutants entering the sea in Haikou City. The results show that in 2017, the fluxes of TN and TP in Haikou were 11610 tons and 1074 tons respectively, of which the local TN and TP contribution fluxes into the sea accounted for 45.5% and 58.7% respectively. Sewage discharge and fertilizer application were the main sources of the local TN flux, accounting for 35.7% and 35.5% of the total, respectively. Agricultural fertilizer was the main source of the local TP flux, accounting for 48.3% of the total. The east coast of Haikou Bay has higher flux intensities of TN and TP, which were 15 t/km² and 1 t/km² respectively. It is suggested that Haikou should strengthen the prevention and control of sewage discharge and fertilizer application pollution, adhere to the coordinated treatment of upstream and downstream of the basin, improve the coverage rate of forest land, increase the retention time of pollutants in the land area, carry out wetland remediation and restoration, increase the absorption of pollutants, reduce the direct discharge of point sources into the sea, and further improve the environmental quality of the coastal waters.