The complex and demanding marine environment poses significant challenges for concrete coatings. Despite the exceptional properties, superhydrophobic coatings have encountered limitations such as complex preparation processes and limited structural stability, thus impeding their widespread application. In this study, we employed molecular monomers to simultaneously conduct in-situ silica mineralization and silane hydrolysis reactions on mortar substrate. The mineralized product, nano-silica, effectively fills microcracks and pores, serving as an internal reinforcing agent. Simultaneously, the silica is utilized to construct a robust and dense micro-nano hybrid structure. The results in the preparation of a silica mineralized layer with exceptional mechanical strength on the surface. The in-situ hydrolysis of silane introduces a low surface energy for hydrophobic modification, leading to the formation of a stable superhydrophobic coating with a contact angle of 157°. Mineralized structure and hydrophobic surface offer both internal and external protective effects. This one-step approach promotes the complete hybridization of hydrophobic silane groups with the three-dimensional silica matrix. During the in-situ reaction process, the hydrolyzed silane molecules bond with the surface of silica microspheres, significantly enhancing the integrity and stability of the coating structure. Notably, even after multiple cycles of peeling and abrasion, the coating surface maintains its hydrophobic properties, further emphasizing its durability. The results demonstrate that this coating enhances both the structural and chemical performance of cement-based materials, paving the way for the expanded application and development of superhydrophobic coatings in the marine concrete industry.