Extensive molecular dynamics simulations of water permeation and ion selectivity of the single-walled carbon nanotubes with the radial deformation are presented. The simulated results indicate that there is a close relationship between the minor axis of deformed carbon nanotubes and the variety, density as well as the position of functional groups. The critical minor axis of different diameter carbon nanotubes exists, and the carbon nanotube whose minor axis is less than the critical minor axis owns the selectivity of chlorine and sodium ions. Meanwhile, compared with intrinsic carbon nanotubes, the deformed nanotubes do not obviously reduce the permeation of water. The analysis of the potential of mean force reveals that the selectivity and the permeation of ions come from the pass potential barrier of carbon nanotubes with various minor axises. Furthermore, our observations of modifying functional groups may have significance for controlling the minor axis and improving the selectivity and permeation of ions in real manufacture of some large nanotubes.