Polydimethylsiloxane/silica (PDMS/SiO2) particle-reinforced nanocomposites prepared at the present study are typical viscoelastic materials. Due to the high surface-to-volume ratio of the SiO2 nanoparticles, the interface effects on the overall properties of the nanocomposites cannot be ignored. In order to investigate the interface effects on the viscoelastic properties of the nanocomposites, a multiscale model is established in the present study, combining the molecular dynamics (MD) model of the interface at the nanoscale and the unit cell model of the nanocomposites at the mesoscale. In the MD model of the interface, the viscoelastic properties of the interphase region influenced by the interface are found to be different from that of the pure PDMS matrix and the bulk SiO2. Because the polymer chains subject to different restrictions existing in the interphase region, this region can possess high stiffness and damping properties simultaneously. The interphase parameters can be determined by the inverse multiscale simulation method, taking advantage of both the numerical model and the experimental results. Due to the interface effects, as demonstrated by the unit cell model, the dynamic shear moduli of the nanocomposites can be simultaneously improved by several times to an order of magnitude higher than that of the matrix, in consistent with experimental results. Thus, the mechanism of the interface effects enhancing the viscoelastic properties of the PDMS/SiO2 nanocomposites can be revealed in the present study, which can be useful for the design of viscoelastic nanocomposites with high stiffness and damping properties.