A scheme of orthogonally polarized laser (OPL) with polarization self-modulation (PSM) in the coaxial end-pumping configuration is proposed in this work. The gain medium consisted of two Nd:YVO4 crystals with orthogonal optical axes, and a quarter-wave plate served as a polarization-switching device. By rotating the electric vector during each cavity round trip, frequency degeneration and correlated operation of two polarization components were achieved. The polarization eigenstates in two orthogonal directions were analyzed using the Jones matrix and eigenequation. The spectral distribution was also briefly discussed based on thermal effects. The results showed that two eigenmodes located at 45° and 135° to the crystal axis, respectively, with a frequency difference equaled to half the free spectral range of the resonator. In the experiments, it was found for the first time that the modulation of eigenstates can be realized by adjusting pump parameters (including pump power, beam size, focusing position, and pump wavelength) and cavity anisotropy, which enables the manipulation of degree of polarization (DOP) and monitoring the resonator properties. Overall, tuning the laser polarization eigenstate offers a flexible method to switch the operational states of the OPL, including the longitudinal mode frequency difference, DOP, polarization angle, etc. It is believed this scheme provides a valuable reference to realize compact, high-beam-quality, and robust OPLs for applications such as dual-frequency light source development, precision measurement and polarization control.