There are many types of concrete protection materials, but silane-based protective materials have excellent performance and durability. Experimental usage of silane sol-based waterproof materials is relatively mature and research studies on microscale mechanisms are relatively sparse. In this paper, molecular dynamics simulations are used to explain the microscopic transmission mechanism by analyzing the transport of water molecules and siloxane molecules in the gel pores, the local structure at the interface, and the molecular dynamics in the pores. Firstly, four models with different concentrations were constructed (0, 0.3, 0.6, and 0.9 mol/L). By comparison, it can be found that as the concentration increases, so does the effect of inhibiting the transport of water molecules in the pores. Based on the determination of the concentration, this paper corrects the arrangement. Next, the three commonly used silanes in the experiment were selected for simulation. It was found that octyltriethoxysilane has good stability and a waterproof effect. Among them, octyltriethoxysilane has a longer alkyl chain and is more stable at the interface, which destroys the original spatial correlation and weakens the capillary adsorption.