To obtaining the influence of non-point source pollution caused by heavy rainfall on the water quality of reservoir, a 3-D hydrodynamic and water quality model is established to analyze the changes in 3-D hydrodynamics and spatial distribution of pollutant concentration in Dahuafang reservoir during heavy rainfall. Result show that in the presence of large inflow, the flow field in reservoir area is mainly affected by inflow and outflow; pollutants migrate and diffuse towards the downstream with the flow process, and the maximum concentration and influence range increase and then decrease with the passing of time. When inflow gradually reduces, the influence of stream flow on reservoir flow field gradually weakens while the effect of wind-driven flow gradually intensifies, which suggest that the flow field is controlled by both the inflow and outflow and the wind-driven flow. In the course of migration, pollutant concentration presents corresponding changing characteristics in three dimensions.