Abstarct: In This study, free vibrations of hetero-junction CNTs were investigated under various boundary conditions at different lengths. This was accomplished by use of molecular dynamics simulations, baxsed on the Lennard-Jones potential energy functions. Hetero-junction CNTs are constructed of two different tubes where pentagon–heptagon pair defects play a significant role in the transition region. These particular CNTs are considerably important baxsed on their outstanding characteristics. In this study, natural frequencies of these hetero-junction CNTs were obtained and compared with the corresponding ones which were calculated from a finite element model. In addition, the computational results of hetero-junctions were obtained and also compared with their constituent homogeneous CNTs. It has been shown that the natural frequency of straight hetero-junction CNTs was greater the one of their constituent CNTs with the same length where the wider tube had a clamped boundary condition. But, for the case where thinner tube was clamped, the natural frequency was lower than their constructive nanotubes with the same length. The frequency of Hetero-junction CNTs was decreased as the length was increased. Furthermore, increasing the nanotube diameters was caused increasing the frequency of hetero-junction CNTs. In this research, the coaxial junctions were also examined and compared with their common type. It was seen that this configuration would lead to increasing their natural frequency. Also, for a typical joint, the effect of temperature on the natural frequency was studied and it was observed that increasing temperature resulted in increasing the natural frequency, only where the wider tube was clamped. Finally, in this study, the effect of the cavity defect in the region of junction on the natural frequency was investigated and some important results were obtained.