Through the molecular dynamics simulations, the ionic currents in physically realistic nanochannels with consideration of the thermal motion of channel walls are observed. It is found that the ionic current changes a little as the surface charge density increases from 0 to −0.3C/m2 with a huge decrease at −0.3C/m2 when the electric filed strength is 0.25V/nm. The Cl-ion current shows a decrease-increase profile as the surface charge density increases, while there is an increase-decrease trend in the Na+ ion current with the turning point at −0.075C/m2. By the statistic of the concentration and velocity distributions, the location of Na+ ions which provide main contribution to the current moves from the center of the channel to the charged surface as surface charge density increases from 0 to −0.225C/m2. The two parts included in current carriers have different concentrations and mobility. So the different contributions of the two parts Na+ ions and Cl-ions cause the feature of ionic current.