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We present an ultrasonic method for determining the thickness of a composite consisting of a soft thin film attached to a hard plate substrate, by resonance spectra in the low frequency region. The interrogating waves can be incident only to the two-layered composite from the substrate side. The reflection spectra are obtained by FFT analysis of the compressive pulsed echoes from the composite, and the thicknesses of the film and the substrate are simultaneously inversed by the simulated annealing method from the resonant frequencies knowing other acoustical parameters in prior. The sensitivity of the method to individual thickness, its convergence and stability against experimental noises are studied. Experiment with interrogating wavelength 4 times larger than the film thickness in a sample of a polymer film (0.054 mm) on an aluminium plate (6.24 mm) verifies the validity of the method. The average relative errors in the measurement of the thicknesses of the film and the substrate are found to be -4.1% and -0.62%, respectively.