In this paper, the frequency difference of the eigen polarization modes of the Nd:YAG crystal laser at different polarization ratios is experimentally studied, and to the best of our knowledge, the correlation between the frequency difference of the eigenmodes and the output polarization degree is reported for the first time. Combined with the analysis of the polarization beam profile, it is proved that the polarized laser produced by the isotropic crystal is due to the frequency locking of the eigen polarization modes. The weak birefringence in the crystal causes the round-trip phase difference of the orthogonal polarization modes, which leads to the frequency difference between the polarization modes. By the adjustment of the cavity mirror, the anisotropic loss will interact with the round-trip phase difference. The eigen polarization modes can reach frequency degeneration, and then be coherently combined to produce linearly polarized laser output. This work provides a useful reference for understanding the physical mechanism of polarized lasers realized by isotropic crystals.