The determination of pollutant reduction cost in the ecological compensation method for pollutant flux neglects the differences in various pollutant sources, and the estimation of pollutant flux does not consider the actual hydrology and characteristics of water quality within a year. Hence, the above method is improved based on the two aspects, namely, the cost of pollutant reduction and the total amount of pollutant discharges. The pollutant reduction costs are divided into two parts: point sources(mainly industrial wastewater, urban domestic sewage)and rural non-point sources(mainly rural domestic sewage, agricultural production sewage). The final costs of reduction are weighted according to the proportion of pollutant emissions. At the same time, the water period within the year is divided, and the flux of pollutants is calculated separately. A case study is carried out to validate the proposed method in the buffer zone between Chongqing and Sichuan on Laixi River, a branch of Tuojiang River. The results indicate that the calculated amount of compensation can essentially reflect the regional pollution characteristics and it is more realistic and credible,