In studies of ion channel systems, due to the huge computational cost of polarizable force fields, classical force fields remain the most widely used for a long time. In this work, we used the AMOEBA polarizable atomic multipole force field in enhanced sampling simulations of single-channel gA and double-channel gA systems and investigated its reliability in characterizing ion-transport properties of the gA (Gramicidin A) ion channel under dimerization. The influence of gA dimerization on the permeation of potassium and sodium ions through the channel was described in terms of conductance, diffusion coefficient, and free energy profile. Results from the polarizable force field simulations show that the conductance of potassium and sodium ions passing through the single- and double-channel agrees well with experimental values. Further data analysis reveals the molecular mechanism of protein dimerization affecting the ion-transport properties of gA channels, i.e., protein dimerization accelerates the permeation of potassium and sodium ions passing through the double-channel by adjusting the environment around gA protein (the distribution of phospholipid head groups, ions outside the channel and bulk water), rather than directly adjusting the conformation of gA protein.