Deviation of aircraft parts is inevitable in the manufacturing process. By analyzing the influences of position deviation of holes on structural stress of bolted joints, this research studied multipin load distribution under different edge margins and obtained detailed stress distribution and concentration. Furthermore, the influence laws of processing method of plugging holes on stress concentration were analyzed based on the two factors, i.e. the diameter of extra holes and the thickness of holeplugging materials. This provides basic data supports for determining the first position of fatigue damages caused by stress concentration occurring on parts with position deviation of holes and estimating fatigue life of parts with position deviation of holes by using nominal stress method.