The thermal effect of laser diode end-pumped double longitudinal mode dual-frequency microchip laser on dual-frequency laser spectrum is investigated in detail. Through solving the heat conduction equation of isotropic material, a general expression of temperature field within Nd:YVO4 microchip crystal is obtained, then the thermally induced refractive index change of microchip laser is analyzed, and thus the thermally induced frequency difference change of dual-frequency microchip laser is calculated. According to the theoretical results, an experiment is designed. The experimental results show that with a small pumping power, astable doublelongitudinal mode dual-frequency is obtained; increasing the pumping power, the thermal effect of crystal makes the frequencydifference decrease gradually, and the width of each mode spectrum broaden. The experimental results are in good agreement with the theoretical analyses.