Abstract In this paper, the Multiscale 3D Representative Volume Element approach is proposed for modeling the elastic behavior of carbon nanotubes reinforced composites with vacancy defects. The Carbon Nanotube has been modeled using atomistic scale by Molecular Structural Mechanics. Space frame structure similar to 3D beams and point masses are employed to simulate the discrete geometrical constitution of the single walled carbon nanotube. The covalent bonds between carbon atoms found in the hexagonal lattices are assigned elastic properties using beam elements. The nodes are treated as Carbon atoms on which the point masses are applied. The vacancy defect is considered in the single wall carbon nanotubes. The matrix phase has been investigated using continuum mechanics approach at macro scale level. The carbon nanotube and matrix regions are connected by interfacial zone using beam elements. Using the proposed multi scale model, the deformations obtained from the simulations are used to predict the elastic modulus of the nanocomposite. The mechanical properties are evaluated for various Vacancy defect locations and number of defects. The influence of the vacancy defects on the chiral CNT reinforced composite is studied under an axial load condition. Numerical equations are used to extract the effective material properties for the cylindrical RVE with non-defective CNTs. The FEM results obtained for non-defective Carbon Nanotubes are consistent with analytical results for cylindrical Representative Volume Element, which validate the proposed model.