In order to quantitatively analyze the nitrogen and phosphorus output flux process of river base flow in Yunnan-Guizhou Plateau area, the minimum sliding method, Chapman-Maxwell filtering, Boughton-Chapman filtering and recursive digital filtering were used to segment the base flow of the Simao River, a tertiary tributary of the Lancang River. Based on the LOADEST model, the nitrogen and phosphorus output flux process of the total runoff and base flow of Simao River were simulated, and the base flow nitrogen and phosphorus output flux contribution were estimated. The results show that:Boughton-Chapman filtering is more effective for the base flow segmentation of Simao River, and the average annual supply of the base flow accounts for about 66% of the total runoff of Simao River. The determination coefficients R²of NH₃-N and TP output flux model equation of Simao River total runoff based on LOADEST model are 81.89% and 72.67%,respectively, indicating a good fitting effect. The average annual output fluxes of NH₃-N and TP are 567.58 t, 25.75 t, respectively. The average annual base flow output fluxes of NH₃-N and TP are 391.57 t and 18.87 t, respectively, which contribute 69% and 73% to the average annual nitrogen and phosphorus total runoff output flux of Simao River, respectively. While doing a good job in reducing nitrogen and phosphorus in the land area, the precise prevention and control of base flow nitrogen and phosphorus pollution should be fully considered.