Chemical functionalization is an effective approach to address interfacial deterioration caused by environmental exposure in cellulose nanofiber (CNF)-epoxy nanocomposites. However, how functionalization affects interfacial deterioration and durability of nanocomposites in erosive environment is still lacked. In this work, the global mechanical properties and local interfacial intermolecular behavior of pristine and functionalized CNF-reinforced nanocomposites are investigated through molecular dynamics simulations. The results show that functionalization can enhance the interfacial energy barrier and debonding stress by 43% and 57%, respectively. Functionalized CNF inhibits the slippage of epoxy chains, ensuring better interfacial adhesion and efficient stress transfer between fiber and matrix. Functional groups promote the formation of interfacial bridging and topological structures and weaken the hydrogen bonding ability of water molecules, leading to stronger intermolecular adsorption effect and better interfacial integrity. The epoxy molecular configuration evolution and intermolecular interactions, caused by the functionalization of CNF in the interfacial region, enhance the interfacial erosion resistance, contributing to the durability of the nanocomposites. This study reveals the in-depth interfacial deterioration mechanism of functionalized nanocomposites under erosive environment, inspiring a novel strategy for the design of durable CNF-reinforced nanocomposites.