Nanobeams have promising applications in areas such as sensors, actuators, and resonators in nanoelectromechanical systems (NEMS). Considering the effects of gyration inertia, surface layer mass, surface residual stress, and surface Young’s modulus, this study develops the vibration equations of the Timoshenko nanobeam. The generalized differential quadrature (GDQ) method and molecular dynamics (MD) simulation are used to study the surface effect on vibration. For a rectangular cross section, surface residual stress and surface Young’s modulus are all affected by the height of the cross section rather than by the length–height ratio. If surface layer mass is considered, then the first three natural frequencies all decrease relative to their counterparts in the case in which surface layer mass is ignored. Results show that the effect of gyration inertia on resonance frequency is negligible. Longitudinal vibration does not easily occur relative to the bending and rotation vibrations of nanobeams. In addition, the results obtained by the GDQ method fit those obtained by MD simulation for beams with length–height ratios of 4–8. This study provides insights into the mechanism of the vibration of short and deep nanobeams and sheds light on the quantitative design of the elements in NEMSs.