This paper reports the measurement of the thermal diffusivity of thin films on substrate by the photoacoustic method. In order to examine the method, we built a new apparatus and proposed (1) a system calibration procedure using thermally thick materials and (2) a data analysis procedure based on the Rosencwaig and Gersho theory (RG theory). As a result of using a transparent photoacoustic cell, the systematic error factors which were caused by stray light have been reduced. With this apparatus, measurements have been performed on platinum, titanium and stainless steel (SUS304) thin foils (thickness: 50-100μm) with three different substrate materials (water, glycerol, and ethyl alcohol). The reproducibility was within ±7% regardless of the film thickness and substrate material.