In this paper, the macroscopic and microscopic deformation caused by sodium penetration in the carbon cathode has been studied during aluminum electrolysis. The distributions of sodium concentration in the carbon cathode has been measured by SEM-EDS. The microstructure change caused by the gradient of the sodium concentration in the carbon cathode has been studied using transmission electron microscopy (TEM). The results indicate that sodium penetration decreases with the increase of the penetration depth. The stresses caused by the gradient of the sodium concentration result in a remarkable change for the microstructure of the carbon cathode. The formation of dislocations resulting in dislocation arrays and the development of kink band networks bring about material damage growth and possibly subsequent weakening of the cathode. These results can provide useful information that is helpful in developing an improved comprehending of the microscopic deformation mechanism of the carbon cathode during aluminum electrolysis.