In this paper, free vibrations of non-uniform multi-scale nanocomposite beams reinforced by carbon nanotubes (CNTs) are studied. Mori-Tanaka (MT) technique is employed to estimate the effective mechanical properties of three-phase CNT/fiber/polymer composite (CNTFPC) beam. In order to obtain the natural frequencies of structure, the governing equation is solved by means of Generalized Differential Quadrature (GDQ) approach. The accuracy and efficiency of the applied methods are studied and compared with some experimental data reported in previous published works. The influences of volume fraction and agglomeration of nanotubes, volume fraction of long fibers, and different laminate lay-ups on the natural frequency response of structure are examined.