A thermal microscope is a useful tool for investigating the spatial distribution of the thermal transport properties of materials. However, for materials with relatively high thermal effusivities, it is well known that the values calculated on the basis of the conventional one-dimensional heat flow solution are higher than the values provided in the literature. In this study, we developed a simple calibration procedure for a thermal microscope to measure the thermal effusivities of materials by using several reference materials whose thermal effusivities are known. It is expected that the temperature response will be influenced by not only the thermal effusivity but also the heat capacity per unit volume. However, reference samples with different heat capacities per unit volume were used. In comparison with the calculated values obtained with the conventional one-dimensional heat flow solution, the values for pure iron obtained with our calibration procedure, without considering the heat capacity per unit volume, were closer to the values provided in the literature. We found that this procedure is useful for calibrating a thermal microscope easily for measuring thermal effusivity.