Configurations of single-walled carbon nanotubes (SWCNTs) with randomly distributed vacancies were generated by numerical method. Molecular dynamics (MD) method was used to investigate the compressive mechanics properties of SWCNTs with vacancies. The simulation results show that the SWCNTs with vacancies have more complicated deformation procedures and the Young’s modulus is lower than the corresponding perfect SWCNTs. The Young’s modulus of the SWCNTs with no more than 20 vacancies ranges from 940Gpa to 620Gpa, and its value is approximately linearly proportional to the number of vacancies. It is found that local buckling first appears in the surface region having high density of vacancies of (10, 10) SWCNTs under axial compression. As the loading increases, SWCNTs with more vacancies have more complicated buckling configuration and sluggish energy variation. Under a case of the same displacement load the more vacancies the SWCNT has, the more complicated the mechanical behavior is. SWCNTs with 20 vacancies can still maintain self structure stabilization, this validates that SWCNTs have good spacial stabilization.