This study presents a model for simulating the microscopic heat transfer processes in a wood-metal composite material. The model was developed by analyzing the microstructure of experimental samples comprising a melted alloy impregnated in a wood matrix. According to the thermal parameters of the materials and the boundary conditions, an analytical model of microscale heat transfer was established using Abaqus finite element analysis software. The model was validated experimentally by comparing temperature curves obtained via simulation and experiments; the resulting correlation coefficient was 0.96557. We then analyzed the temperature distribution of the composite material with different cell geometries and heat transfer conditions (heat transfer direction and applied temperature). The thermal properties of the unit cell models were in good agreement with the general trends predicted by several heat transfer equations. This study provides a method for analyzing the microscale heat transfer process in wood-based composites. In addition, the model framework characteristics can be used to evaluate the heat transfer mechanism of impregnated modified wood.