The hydrated calcium silicate (C-S-H) gel is the main hydration product and source of paste strength of cement. In this paper, molecular dynamics simulation method based on ClayFF was used to investigate the effect of micropore direction on the fracture performance of C-S-H under tensile load and interpret the micro deformation, fracture, and failure processes of cement concrete. After establishing a complete C-S-H model with chemical formula (CaO)1.60(SiO2)(H2O)1.57 and micropore models with different pore sizes and directions, the influence of micropore direction on the fracture performance of the C-S-H models was analyzed from three perspectives: mechanical property, micro fracture process, and energy evolution. It was found that the ultimate stress and Young’s modulus of the C-S-H models showed a decreasing trend with the increase of micropore size, and were less affected by the direction of micropores. It was also found that the direction of micropores had a significant impact on the structural failure of the C-S-H models in the x direction tensile simulation, followed by the y direction, and had the smallest effect on the z direction. It was also found that the elastic energy and input energy of the C-S-H models exhibited decreasing trends with the increase of pore size, and the three-dimensional critical energy release rates of different pore models’ difference also decreased.