Recently, various kinds of micro- and nanofluidic functional devices have been proposed, where a large surface-to-volume ratio often plays an important role in nanoscale ion transport phenomena. Ionic current analysis methods for ions, molecules, nanoparticles, and biological cells have attracted significant attention. In this study, focusing on ionic current rectification (ICR) caused by the separation of cation and anion transport in nanochannels, we successfully induce electrodiffusioosmosis with concentration differences between protons separated by nanochannels. The proton concentration in sample solutions is quantitatively evaluated in the range from pH 1.68 to 10.01 with a slope of 243 mV/pH at a galvanostatic current of 3 nA. Herein, three types of micro- and nanochannels are proposed to improve the stability and measurement accuracy of the current–voltage characteristics, and the ICR effects on pH analysis are evaluated. It is found that a nanochannel filled with polyethylene glycol exhibits increased impedance and an improved ICR ratio. The present principle is expected to be applicable to various types of ions.