CEMHYD3D is an advanced, three-dimensional computer model for simulating the hydration processes of cement, in which the microstructure of the hydrating cement paste is represented by digitized particles in a cubic domain. However, the system resolution (which is determined by the voxel size) has a prominent influence on the simulation results and, thus, is difficult to choose a priori. In this paper, it is shown that the effects of system resolution on the simulation results are mainly due to the lack of considerations of the diffusion-controlled reactions in the model. A new concept “hydration layer” is proposed for mitigating the effects of system resolution on the model predictions. By performing simulations with different system resolutions, the robustness of the improved model is demonstrated. Comparisons of model predictions with experimental measurements further demonstrate that the use of hydration layer can successfully mitigate the bias brought by the system resolution.