Taking a reservoir in South China as an example, we use rainfall-runoff unit hydrograph method to analyze the time changing process of surface runoff inflow, which generated by typical design rainfall. On the basis of time series data of flow and water quality in control section of the main rivers in Xili Reservoir, we establish mathematical response relation between non-point source pollutants flux, such as flux of COD, flux of NH3-H, in catchment area of control section and runoff. Then we simulate the time dynamic change progress of non-point source pollution load which generate with the initial stage runoff that generated by design rainfall and flow into reservoir. It can provide technical parameters for the design of non-point source which generate from early runoff treatment project.