Internal information such as mechanical properties and geometrical structures of non-transparent materials can be obtained non-destructively by means of a laser ultrasonic technique. The laser ultrasonic technique measures time of flight of an ultrasonic acoustic pulse generated at the surface of the materials by a pump pulse laser where the acoustic pulse is reflected from the internal structures of the material. The time of the flight of the acoustic pulse can be measured by the time-sequential modulation of the reflectance of a probe laser that is irradiated on the surface of the material. Assuming that the material has a structure of multilayer, each thickness of the multilayer can be reconstructed by fitting of numerical calculations of the time-sequential modulation of the reflectance to the experimental measurements with fitting parameters of the thicknesses. The numerical calculation, however, should solve the spatial distribution of the absorbed energy of the pump laser which determines the shape of the acoustic pulse, the strain tensor of the acoustic pulse, and the reflectance of the probe laser. It likely follows that the three different numerical calculation methods are necessary. Then, an efficient numerical calculation method for the reconstruction of the multi-layer structure using FDTD (Finite Difference Time Domain) algorithm where the method can be applied to the above-mentioned three different calculations in the same frame is proposed here.