A microstructure model combined with diffusion-based mechanism is reconstructed. The objective is to propose a model that could describe the long-term microstructure evolution driven by certain physical mechanisms. With modifications in parametric control, the introduced kinetics is extended to directly consider the particle size distribution (PSD) of cement (alite). The particle impingement is analyzed for the effects of PSD and water-to-cement ratio (w/c ratio). The variations of C-S-H bulk density and hydrates distribution under different temperature are explored in the microstructural modeling. Numerical results for effects of PSD, w/c ratio, temperature, as well as the ambient humidity are obtained and compared with experimental results. Validations especially for early hydration prove that the current model could capture characteristics regarding hydration and evolved microstructure from hours to years.