Synthesis of hybrid nanotubes to overcome the drawbacks of individual pure nanotubes in order to apply them in novel nanodevices has attracted great interest of researchers. To this end, pure single-and double-walled boron nitride nanotubes together with carbon and boron nitride double-walled hybrid nanotubes are simulated through molecular dynamics simulations in order to study their vibrational behavior. The natural frequency of nanotubes is computed, and the effects of geometrical parameters and boundary conditions on the natural frequency are investigated. According to the generated results, the natural frequency of boron nitride nanotubes is higher than that of their carbon counterpart and nanotubes with clamped boundary conditions possess the highest natural frequency compared to other types of boundary conditions. Also, the natural frequency of double-walled hybrid nanotubes is found to be between those of pure double-walled boron nitride and carbon nanotubes with small lengths. It is found that the natural frequency of double-walled hybrid nanotubes is less sensitive to length increase compared to pure double-walled carbon and boron nitride ones, leading to higher frequencies at greater lengths. Finally, to study the variation in natural frequency with the length, a rational curve is fitted to each data set and the corresponding constants are computed.