As reinforcing nano-fillers, graphene nanoplatelets (GNPs) have shown considerable promise for developing high-performance cement composites. However, the influence of GNP orientation and pores on the compressive and damage evolution of the GNP reinforced cement composites (GNPRCCs) remains unclear. This work employs three-dimensional finite element modeling along with experiments to provide fundamental insights into the property-microstructure relationships in the GNPRCCs. The model which incorporates GNP and pore as individual phases with cohesive interactions is developed and validated. The simulations reveal that the alignment of GNPs at 45° has the most significant effect on improving the load-bearing capacity and damage resistance of the GNPRCCs. A larger GNP diameter-to-thickness ratio is more beneficial for enhancing crack bridging and propagation control. The orientation and porosity of pores are evidenced to have significant effects on the damage behaviours of the GNPRCCs, where the pore shape shows negligible effects. These findings elucidate the underlying mechanisms that underpin the mechanical behavior of GNPRCCs, providing key guidelines to tailor and optimize the microstructural features for advanced construction materials with superior performance and durability.