The integrity of organic-inorganic interface determines the performance of composite material systems, such as concrete reinforced with basalt fiber reinforced polymer. The integrity of the interface, which depends on the epoxy resin, may be degraded in harsh environments such as in seawater and concrete alkaline environments. In this study, a novel resin cross-linked with polydimethylsiloxane (PDMS) was developed to enhance the performance of composite material in harsh environments. The long-term mechanical strength of the composite (after modification to enhance its hydrophobicity) increased by 20% in concrete alkaline environments, based on micro- and macro-experiments. This improvement is attributed to cross-linking between PDMS and epoxy molecules and the formation of PDMS phase-separated circular domains, which achieve dynamic equilibrium and simultaneously enhance the densification and hydrophobicity. Molecular dynamics simulations revealed that PDMS reinforces interface adhesion and significantly improves the corrosion resistance by facilitating covalent bond formation at the resin-fiber and even resin-concrete interfaces. This study provides a feasible strategy and atomic insights for durability enhancement of composite with similar organic-inorganic interfaces in concrete structures, thus advancing the safety and service life in marine engineering.