Efficient modelling approaches capable of predicting the behavior and effects of nanoparticles in cement-based materials are required for conducting relevant experiments. From the microstructural characterization of a cement-nanoparticle system, this paper investigates the potential of cell-based weighted random-walk method to establish statistically significant relationships between chemical bonding and diffusion processes of nanoparticles within cement matrix. LaSr0.5C0.5O3 (LSCO) nanoparticles were employed to develop a discrete event system that accounts for the behavior of individual cells where nanoparticles and cement components were expected to interact. The stochastic model is based on annihilation (loss) and creation (gain) of a bond in the cell. The model considers both chemical reactions and transport mechanism of nanoparticles from cementitious cells, along with cement hydration process. This approach may be useful for simulating nanoparticle transport in complex 2D cement-based materials systems.