In this paper, a thermal effusivity calibration procedure is proposed using a numerical calculation and measurement of a phase lag of a thermoreflectance signal based on a periodic modulation thermoreflectance method for a thermal microscope. To improve the accuracy of the estimated thermal effusivity, the profile determination of the heating and probing laser beams and the numerical calculation of phase lags with a two-layer model in a three-dimensional heat conduction equation are carried out. Results of the experiments of beam profile determination and numerical calculation showed that the estimated values of thermal effusivities are in good agreement with the standard values of silicon, germanium, and Pyrex® samples. We are convinced that the use of a thermal microscope with numerical calibration is becoming an accurate and precise thermal property measurement technique for the microscale range.