Considering the influence of the probe beam size on the modulated photothermal reflectance (MPR) signal, a three-dimensional theoretical model of laser-induced MPR for the thin film-on-substrate system is presented in this paper. The feasibility of measuring the thermal parameters on thin films by MPR techniques is investigated. The effects of the material parameters on MPR signals are discussed in detail. The numerical multiparameter estimation of thermal properties is also performed in this paper using the frequency response of MPR signals (i.e. MPR frequency scanning method). Three thermal parameters, i.e. the film′s thermal diffusivity, the substrate′s thermal diffusivity and the thermal resistance on the film-substrate boundary, are simultaneously determined. It is shown that, comparing with the conventional MPR radial scanning method, there is no strong correlation among the three thermal parameters in MPR frequency scanning model. Therefore the convergence and the accuracy of multiparameter estimation for samples can be improved by MPR frequency scanning method.