We propose single-atom catalytic oxidation method for production of subnanometer-scale windows on the graphene layer of single walled carbon nanotubes (SWCNTs) in this study. We used the free-standing SWCNT films which had merits for reliable measurements and applicability to electrochemical measurements for determination of the nanowindow size. Copper(II) 2,3,9,10,16,17,23,24-octakis(octyloxy)-29H,31H-phthalocyanine (CuPc) was adsorbed on SWCNT bundles using liquid-phase adsorption at surface coverage of 0.9. Then, nanowindows were produced by oxidation above 550 K being higher than the decomposition temperature of the bulk CuPc. The oxidation of CuPc-adsorbed SWCNT film markedly increased the surface area from N2 adsorption at 77 K due to access of N2 to the internal tube space through the nanowindows. The nanowindow size was estimated to be the molecular size of N2 through the evident low-pressure adsorption hysteresis of the N2 adsorption isotherm and TEM observation. The selective ion permeability through the nanowindows for H3O+, Li+, Na+, K+, Mg2+, Ca2+, and Ba2+ ions was determined by the inside-capacitance being the capacitance difference of SWCNT between with and without nanowindows. The selective permeation of the hydrated ions depended on the oxidation conditions for production of nanowindows, showing less than 1 nm of the nanowindow size. The relationship between the inside-capacitance and hydrated ion diameter for the selective permeation of hydrated ions indicated partial dehydration of the hydrated ions just only on their permeation through the nanowindows under the accelerated conditions.