A method of axially aligning a charged particle beam implemented by a charged particle beam system equipped with an astigmatic correction lens including a first pair of coils and a second pair of coils. The method starts with obtaining first to sixth sets of image data while varying currents flowing through the first to fourth coils according to first to sixth sets of conditions. Then, the values of the currents through the first to fourth coils for correcting the position of the axis of the beam are calculated based on the first to sixth sets of image data.