The ability to sieve ions through nanopores with high throughput has significant importance in seawater desalination and other separation applications. In this study, a plasma etching process has been demonstrated to be an efficient way to produce high-density nanopores on graphene membranes with tunable size in the sub-nanometer range. Besides the pore size, the nanopore density is also controllable through adjusting the exposure time of the sample to argon or oxygen plasma. The plasma-treated graphene membranes can selectively transport protons, Na+ and Cl- ions. Density function theory calculations uncover that the sp3 and vacancy-type defects construct different energy barriers for different ions, which allow the defected graphene membrane to selectively transport ions. Our study indicates that oxygen plasma etching can be used as a very convenient and efficient method for fabricating a monolayer filtration graphene membrane with tunable sub-nanometer pores.