With the rising demand for epoxy materials for use in structural and coating applications in marine environments, it is necessary to improve the inherently poor properties such as seawater resistance and toughness by the addition of appropriate modifiers. Herein, a composite filler composed of silica nanoparticles (NPs) and poly(ethersulfone) (PES) is demonstrated for the fabrication of an epoxy composite. The composite filler is synthesized via a simple reaction between the amine groups in aminated PES and the epoxide groups in the glycidoxypropyl trimethoxysilane (GPTMS)-treated silica NPs, resulting in a silica–PES core–shell NPs ([email protected]) composite. These epoxy nanocomposites exhibit improved flexural strength and fracture toughness due to incorporation of silica NPs as well as covalently linking PES to epoxy. In addition, the flame retardancy and seawater resistance of the [email protected]/epoxy nanocomposites are significantly improved by the thermally and chemically robust PES and silica NPs.