The modified Gamma distribution and Mie scattering theory were used to examine the light scattering attributes of water cloud particles to investigate the effect of water cloud on quantum interferometric radar (QIR) performance parameters, and a relationship was developed between water content and extinction coefficient of four common water cloud particles. For the polarization state of light quantum, the polarization change law of QIR detected photon under the background of water cloud particles is researched, and the mathematical model of the effect of water cloud particles on the transmission distance, resolution, bit error rate, and the survival performance of QIR detected photon is established. The theoretical analysis and experimental simulation results show that the extinction coefficient linearly increases with the increase of water content in the water cloud, causing the increase of attenuation coefficient, thus increasing the energy dissipation of the detected photon and decreasing the transmission distance of the detected photon. When the number of emitted photons remains constant, the resolution of QIR decreases with the increase in the optical thickness of water cloud particles. When the concentration of water cloud particles remains constant, the bit error rate of the system decreases with the increase of the depolarization ratio. When the number of detectable points of the target is constant, the greater the interference intensity of the water cloud to the QIR system is, the lower the survival performance of the radar is. To improve the detection performance of the system, each index parameter of the QIR system should be adjusted adaptively according to the relevant parameters of the water cloud in the design, debugging, and use of QIR.