Energy transport in silicon–aluminum composite thin films due to short-pulse laser irradiation is examined. Frequency dependent phonon transport in the silicon film is considered to formulate equivalent equilibrium temperature while modified two-equation model is used in the aluminum film to obtain electron and phonon temperatures. Thermal boundary resistance across the films is incorporated in the analysis. Transmittance, reflectance, and absorption of the incident laser beam are determined using the transfer matrix method. Equivalent equilibrium temperatures resulted from frequency dependent and frequency independent solutions are compared. It is found that phonon temperature increase at the aluminum interface is suppressed by phonon transport to the silicon film, which is more pronounced at low laser pulse intensities. The influence of the ballistic phonons on equivalent equilibrium temperature in the silicon film is found to be significant.