The pH plays a key role in the hydration process of cement clinker and thus determines the morphology and mechanical performance of cement-based materials. Herein the effect of pH on the nucleation rate, morphology, and mechanical performance of calcium-silicate-hydrate (C-S-H) gel was explored by performing grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulation. The results show that the packing fraction of C-S-H gel increases correspondingly as the pH increases. Concerning the morphology of C-S-H gel, the results of specific surface area, coordination structure, cluster size distribution, and pore size distribution indicate that with the increase of pH, the spatial distribution is more heterogeneous and the shape of cluster changes from fibril-like to spherical. In addition, as the decrease of pH, the particles are distributed uniformly thus leading to the increase of mechanical properties. These results acquired from this mesoscale simulation provide insights into the role of pH during cement hydration which is a vital step connecting the nanoscale characterization to its engineering application and designing high-performance cement-based materials.