Heat transfer performance of metal foam relies greatly on fluids flow direction due to the presence of the complex micropores in the skeleton. In this work, to explore the effect of different direction micropores in skeleton on the flow and heat transfer, a pore-scale simulation is performed after the reconstruction of realistic three-dimensional metal foam structures. The heat transfer performances of the metal foam with micropores in X- and Y- directions are calculated and compared with the structure without micropores. Results show that the pressure drops of the structure owning X-direction micropores are 4.52%–6.47% lower than those in the structure without micropores, while the pressure drops of the structure owning Y-direction micropores are 0.54%–0.88% higher. The heat transfer coefficients of the structure owning X-direction micropores are 1.39%–3.29% higher than those of the structure without micropores, while the structure owning Y-direction micropores are 0%–1.94% higher. The comprehensive heat transfer factors of the structure owning X-direction micropores are 2.96%–5.62% higher than those of the structure without micropores. The above findings can help design a high comprehensive heat transfer performance of metal foam using the different direction micropores in skeleton structure.