A method of axis alignment for a charged particle beam apparatus comprising a charged particle optical system including an objective lens for focusing a charged particle beam with a lens current I, an aligner (51, 53) for deflecting the axis of the charged particle beam by a deflection angle WAL1', and a detector for detecting a secondary signal generated from a sample due to the irradiation of the charged particle beam, wherein the charged particle beam apparatus is adapted to obtain an image based on a signal from the detector, the method comprising: obtaining a first image in a condition where the aligner deflects the charged particle beam with a first deflection angle WAL1 1 ' and the objective lens focuses the charged particle beam with a first lens current I 1; obtaining a second image in a condition where the aligner deflects the charged particle beam with the first deflection angle WAL1 1 ' and the objective lens focuses the charged particle beam with a second lens current I 2; obtaining a third image in a condition where the aligner deflects the charged particle beam with a second deflection angle WAL1 2' and the objective lens focuses the charged particle beam with the first lens current I 1; obtaining a fourth image in a condition where the aligner deflects the charged particle beam with the second deflection angle WAL1 2 ' and the objective lens focuses the charged particle beam with the second lens current I 2; obtaining a first image deviation ΔW1 that is a parallax between the first image and the second image; and obtaining a second image deviation ΔW2 that is a parallax between the third image and the fourth image; characterized by determining the optimal deflection angle WAL1' of the aligner from the equation WAL 1 ′ = A 1 / B 1, where A1 and B1 are calculated from the two equations ΔWi = ΔI ⋅ A 1 + WAL 1 i ′ ⋅ B 1 for i = 1, 2, where Δ1 = I 1 - I 2 is the lens current difference. obtaining a first image in a condition where the aligner deflects the charged particle beam with a first deflection angle WAL1 1 ' and the objective lens focuses the charged particle beam with a first lens current I 1; obtaining a second image in a condition where the aligner deflects the charged particle beam with the first deflection angle WAL1 1 ' and the objective lens focuses the charged particle beam with a second lens current I 2; obtaining a third image in a condition where the aligner deflects the charged particle beam with a second deflection angle WAL1 2' and the objective lens focuses the charged particle beam with the first lens current I 1; obtaining a fourth image in a condition where the aligner deflects the charged particle beam with the second deflection angle WAL1 2 ' and the objective lens focuses the charged particle beam with the second lens current I 2; obtaining a first image deviation ΔW1 that is a parallax between the first image and the second image; and obtaining a second image deviation ΔW2 that is a parallax between the third image and the fourth image; determining the optimal deflection angle WAL1' of the aligner from the equation WAL 1 ′ = A 1 / B 1, where A1 and B1 are calculated from the two equations ΔWi = ΔI ⋅ A 1 + WAL 1 i ′ ⋅ B 1 for i = 1, 2, where Δ1 = I 1 - I 2 is the lens current difference.