A sensitivity experiment has been performed by MM5v3 model both with and without surface fluxes and both with and without boundary layer, the results show that the effects of surface fluxes and boundary layer are similar, the effect of surface fluxes is the main part. Generally speaking, if the effect of PBL is excluded, the distributions of moist-potential vorticity, moist flux divergence, vorticity and low level jet will change, the location of their centers will change, their strengths also will change (usually decrease),which result in the decrease of precipitation and the change of its location. The boundary layer influences the heavy rain through the total effects of wet potential vorticity, moist flux divergence, vorticity and low level jet, affects the area and intensity of heavy rain.