Calcium silicate hydrate (CSH) plays a crucial role in concrete by controlling its properties and durability. The degradation of CSH often signifies concrete damage. Polydimethylsiloxane (PDMS) is commonly used to protect concrete from sulfate corrosion; however, the comprehensive mechanistic understanding of its protective effects against CSH remains limited. Here, molecular dynamics (MD) simulations were employed to explore atomic-scale interactions between PDMS coatings and CSH in a sulfate-rich environment. Our results reveal that PDMS mitigates sulfate-induced CSH decalcification by forming a positively charged layer, ultimately reducing sulfate bonding by 83.3% compared to the blank group. Molecular structure analysis highlights key hydrogen bonding and calcium–oxygen bonding interactions that are critical for this protection. Higher polymerization stabilizes substrate adsorption, reducing surface diffusion to 33.3% of low-polymerization PDMS, thereby enhancing protection. Additionally, water molecule interactions with the CSH matrix are negatively correlated with the amount of adsorbed sulfate. Simulation results offer valuable insights into the molecular-level dynamic response of the material, contributing to a deeper understanding of the protective mechanisms of PDMS against sulfate-induced CSH degradation in concrete. These findings can guide experimenters and engineers in designing more effective protective coatings for concrete exposed to sulfate-rich environments, thereby laying a foundation for further experimental research and the development of concrete materials with enhanced durability under challenging environmental conditions.