Abstract: The area above the Cuntan section in the main stream of the Yangtze River was divided into 39 output units, and the river network was divided into 63 input rivers. In addition, a topological relationship between units and rivers was built. Based on the steps of production, arrival, and reduction of pollutants, the flux of pollutants at Cuntan section was estimated. The production of pollution from various types of pollution discharge units was checked by export coefficient method. Pollutant arrival coefficient formulas were established and checked considering the effect of precipitation and input amount from point sources and non-point sources. The established coefficients from pollutant carrying sections to output sections were checked considering comprehensive degradation of pollutants in rivers. Contribution rates were analyzed for each pollutant source for each pollutant carrying joints to downstream sections. The model was applied to account for the flux of pollutants and to analyze the contribution rate from tributaries at the Cuntan section in the main stream of Yangtze River from 2004 to 2005. The accounting results show that the monthly loading curve of COD_Mn and TP at the Cuntan section tallies with the measured data well, but that of TN is lower than the measured data, perhaps due to neglected atmospheric nitrogen precipitation. The COD_Mn contribution rate to the Cuntan section of Jialing river was smallest; the general contribution rate was about 14%, among which 6% were from point sources and 8% were from non-point sources, therefore the ratio of non-point sources to point sources was only 1.3. The COD_Mn contribution rate to the Cuntan section of Jinsha river was largest; the general contribution was about 49%, among which 14% were from point sources, 35% were from non-point sources, therefore the ratio of non-point sources to point sources was 2.5, indicated that non-point pollution sources were more serious. As a result, control of non-point sources is more important in Jinsha river.