Fiber-reinforced polymer (FRP) is extensively utilized across various engineering disciplines for its superior properties, including its roles in protecting, reinforcing, and repairing structural components. In marine geotechnical engineering, the interfacial interactions between FRP and soil are crucial, yet they remain poorly understood at the micro- and nano-scale. Molecular dynamics (MD) simulation method has been employed to explore the interfacial mechanical behavior of the epoxy-quartz interface within the context of FRP-soil systems. The MD models were validated through uniaxial tension tests conducted on bulk epoxy. Subsequent MD nanoindentation simulations examined the epoxy-quartz interface, considering the effects of loading rate and indentation depth. An abrasion model for the epoxy-quartz system was proposed based on the relationship between force and displacement. The simulation results indicated that increased loading rates lead to higher indenter forces and greater indentation hardness of the epoxy substrate, with a power-law relationship observed between indenter force and indentation depth. Additionally, the study determined the overall Young's modulus of the bulk epoxy to be 2.075 GPa, with an average Poisson’s ratio of 0.377. For the epoxy substrate, the reduced modulus was 2.419 GPa, and the indentation hardness ranged from 1.492 to 2.174 GPa.