Microchip laser can output two orthogonal frequency splitting modes due to its own internal residual stress. In this paper it is found that the frequency difference of microchip laser is modulated by laser feedback. The modulation is a sinusoid-like curve whose center is the original frequency difference and period is half-wavelength. The amplitude of the modulation curve is proportional to feedback level. But when the feedback is too strong, so that the polarization switching occurs and only one polarization exists sometimes. In a range of external cavity, the amplitude of the modulation curve is also proportional to original frequency difference. The theoretical analysis and simulation based on the composite laser cavity theory and self-consistent theory are in good agreement with the experimental results. The potential applications of this phenomenon in precision measurement are discussed.