An integrated multiscale framework combining hydration kinetics and lattice modeling was established to investigate the microstructural evolution of cement paste. To overcome the inherent overestimation of pore connectivity in traditional models, a nucleation-and-growth mechanism coupled with a small capillary pore redistribution algorithm was incorporated into the generation of representative volume elements featuring polydisperse particles. This approach ensures that the simulated pore network characteristics, such as pore size distribution and percolation threshold, closely align with authentic microstructures. Experimental validation using nuclear magnetic resonance confirms the accuracy of the simulated porosity development. Quantitative structural analysis revealed that, in systems with low water-to-cement (w/c) ratios, connectivity reduction accelerates and tortuosity increases rapidly as hydration progresses, whereas high w/c ratio systems exhibit significantly more gradual variations. Furthermore, both connectivity and tortuosity demonstrated strong correlations with capillary porosity but negligible direct dependence on initial w/c ratios. The derived fitting curves for these structural parameters provide a robust mechanistic basis for durability assessment and service-life prediction of cementitious materials.