During cement hydration, C–S–H nanoparticles precipitate and form a porous and heterogeneous gel that glues together the hardened product. C–S–H nucleation and growth are driven by dissolution of the cement grains, posing the question of how cement grain surfaces induce spatial heterogeneities in the formation of C–S–H and affect the overall microstructure of the final gel. We develop a model to examine the link between these spatial gradients in C–S–H density and the time-evolving effective interactions between the nanoparticles. Using a combination of molecular dynamics and Monte Carlo simulations, we generate the 3D microstructure of the C–S–H gel. The gel network is analyzed in terms of percolation, internal stresses, and anisotropy, and we find that all of these are affected by the heterogeneous C–S–H growth. Further analysis of the pore structure encompassed by the C–S–H networks shows that the pore size distributions and the tortuosity of the pore space show spatial gradients and anisotropy induced by the cement grain surfaces. Specific features in the effective interactions that emerge during hydration are, however, observed to limit the anisotropies in the structure. Finally, the scattering intensity and specific surface area are computed from the simulations in order to connect to the experimental methods of probing the cement microstructure.