To figure out the effect of rainfall on the free space quantum communication, the effect of rainfall intensity on extinction coefficient is discussed based on the theory of the distribution of raindrops and the Mie scattering theory. The relationship between photon attenuation, channel capacity and rainfall intensity is proposed. The calculation model of channel survival function and transmission distance is established. And the performance parameters of the system are simulated. Simulation results show that, without considering the effect of atmospheric aerosol particles and other circumstances, when the rainfall intensity is 1.46 mm/h, the transmission distance is 3 km, the initial energy of the photon decreases to 50%, the channel capacity is 0.2702, the channel value of the survival function is 0.9122 and the error rate of channel is 1.8×10-8. Thus, the rainfall has different influences on the performance of free space quantum communication, including the cavity of the channel, the survival function and the error rate. Therefore, the parameters should be adjusted adaptively based on the rainfall intensity to improve the reliability of free space quantum communication.