Based on the hydrological and water quality data during 2005-2014, runoff division method, rainfall deduction method and runoff deduction method were used to evaluate the non-point source pollution respectively in the upstream of Lijiang River. Compared with rainfall deduction method and runoff deduction method, the accuracy of runoff division method is the highest. The relationship between pollution load difference and runoff difference in wet and dry period can be described by a linear equation, with R² values greater than 0. 88. The calculated values of pollution load using runoff division method were significantly correlated with the measured values, and the R² reached 0. 91. Compared with NH₃-N and COD_Mn, the ratio of non-point source pollution to total pollution load of TP calculated by the different methods showed strong stability. The Average value caculated by runoff division method showed that the ratio of non-point source pollution to total pollution load of COD_Mn, NH₃-N and TP was 0. 70, 0. 73 and 0. 74 respectively. It shows that non-point source pollution load highly contributes to the water quality in the upstream of Lijiang River.