The combination effect of waviness and vacancy defects on the natural frequency of single walled carbon nanotubes (SWCNTs) is investigated. A model based on molecular dynamics and finite element method has been developed for simulation. For the first time, the effects of boundary condition and waviness shape on the vibrational behaviour of wavy-vacancy defected zigzag SWCNTs are presented. The results indicate that for longer SWCNTs, waviness affects the natural frequency more significantly than vacancy defects. Vacancy defects play a more important role in shifting the natural frequency in clamped-clamped SWCNT compared to the clamped-free structure. While the waviness shape drastically influences the effect of waviness on the natural frequency, it does not affect the effect of vacancy defects considerably.