Vitrimers with dynamic covalent bonds combine the merits of thermosets and thermoplastics, opening up new opportunities for science and industry. The attainment of enhanced mechanical performance without compromising dynamic reprocessability poses a significant obstacle to vitrimer materials. Designing vitrimer nanocomposites from interfacial and structural aspects is promising to solve this problem. Herein, strengthening and toughening of hard epoxy vitrimer using nanosilica have been successfully achieved by introducing interfacial covalent binding and microphase separation. Performing interfacial covalent binding between epoxide-modified silica nanoparticles and hard epoxy vitrimer matrix improves interfacial compatibility and nanoparticle dispersion. Controlling the proportion of silica nanoparticles yields two types of microstructures, including a uniformly dispersed material at low nanoparticle loadings and unique microphase separation at high nanoparticle loadings. Particularly, silica reinforcement accompanied with phase separation exhibits a substantial enhancement in Young’s modulus, tensile strength, and fracture toughness while achieving good stretchability. In addition, the silica-epoxy vitrimer nanocomposites preserve excellent reprocessability not inferior to the pristine vitrimer. The resulting nanocomposites show potential applications in bonding, recycling, and shape morphing. The concepts and methodologies presented in this work will enlighten future vitrimer material design.