We study the polarization distribution model under wavy water surfaces dominated by skylight, verify the feasibility of using polarization navigation under wavy water surfaces, and discuss the influence of different sun positions and wavy water surfaces on the underwater polarization distribution model. The Cox-Munk sea wave model is used to describe the wavy water surface. The underwater polarization propagation model is built on the basis of the Stokes vector and Mueller matrix, which consider the atmospheric Rayleigh scattering, the air-water interface refraction, and the single Rayleigh scattering of water molecules. The consistency between the simulation result and measurement result proves the accuracy of the proposed model. The results show that the wavy underwater polarization distribution model dominated by skylight is predictable, and it is mainly related to the sun position and the wave condition on the water surface. The proposed model can analyze the polarization characteristics of wavy underwater more accurately and provide a theoretical basis for the application of underwater polarization navigation.