This study presents a modified continuum model to investigate the vibration behavior of single and multi-carbon nanotubes (CNTs). Two parameters are exploited to consider size dependence: one derived from the energy equivalent model and the other from the modified couple stress theory. The energy equivalent model, derived from the basis of molecular mechanics, is exploited to describe size-dependent material properties such as Young’s and shear moduli for both zigzag and armchair CNT structures. A modified couple stress theory is proposed to capture the microstructure size effect by assisting material length scale. A modified kinematic Timoshenko nanobeam including shear deformation and rotary inertia effects is developed. The analytical solution is shown and verified with previously published work. Moreover, parametric studies are performed to illustrate the influence of the length scale parameter, translation indices of chiral vector, and orientation of CNTs on the vibration behavior. The effect of the number of tube layers on the fundamental frequency of the CNTs is also presented. These findings are helpful in mechanical design of high-precision measurement nano-devices manufactured from CNTs.