A truck refrigeration system using phase change material (PCM) is expected to have a lower noise level, reduced energy cost, and much lower local greenhouse gas emission. Recently, a forced convection type PCM refrigeration module has been developed. As the operation time increases, the PCM around the air inlet melts, because of a large temperature difference between the PCM and air. Therefore, the latent heat transfer area decreases and the heat transfer rate of the module decreases even though there is a lot of PCM which does not melt around the air outlet. A computational fluid dynamic modeling of the PCM refrigeration module was developed and validated by the experiment. Using the CFD, the design parameters, such as the mass flow rate of the air and roughness of the slab, were investigated to improve the heat transfer inhomogeneity. As a result, the adoption of partial roughness on the slabs improved the heat transfer inhomogeneity and reduced a fan power.