The self-mixing interference in birefringent dual frequency laser is systematically studied for the first time. The output intensities of two orthogonal modes are both modulated by external cavity length, and their phase relationship is experimentally and theoretically demonstrated. When frequency difference is greater than line width of homogeneous broadening gain curve, the phase relationship is determined by phase difference of two modes. If the frequency difference is smaller than the line width, modes competion will play an important role. Our results can advance the research of self-mixing interferometer of orthogonally polarized dual frequency laser.