Abstract: The deterioration of concrete performance leading to structural failure is an important reason for the reduction of engineering safety and service life. Applying protective coatings on the surface of concrete is an important method to improve its performance. Traditional organic coatings struggle to meet long-term protection requirements of concrete due to poor weather resistance and insufficient interfacial compatibility. Although geopolymer coatings exhibit excellent chemical stability and environmental benefits, due to their good hydrophilicity, they are prone to water absorption, swelling, and microcrack propagation, significantly compromising their protective performance. This study proposes a novel method for preparing a hydrophobic geopolymer coating modified with trimethoxy(methyl)silane (MTOS). Combining experimental characterization and molecular dynamics simulations, the hydrophobic mechanism and interfacial properties of the coating were systematically investigated. By optimizing the MTOS content (2%~10%), the variations in coating setting behavior, contact angle, mechanical durability, and interfacial bonding strength were analyzed. The results indicate that the incorporation of MTOS significantly prolongs the setting time, surface drying time, and through-drying time of HGC, while also enhancing its hydrophobicity. When the MTOS content reaches 10%, the contact angle of HGC increases to 130.4°, and remains within the range of 125°–130° even after abrasion resistance testing. However, the interfacial bonding strength between the coating and the cement substrate decreases by 59% (0.23 MPa). A molecular dynamics model controlling the monomer bonding process effectively simulates the geopolymerization reaction. Molecular simulations confirm that MTOS enhances the hydrophobicity of HGC by reducing the surface energy of the coating. This study provides theoretical support and a technical pathway for the development of high-performance geopolymer coatings, offering significant value for engineering applications.