A charged particle beam apparatus facilitating adjusting the beam center axis of a charged particle beam in a case where optical conditions are modified or in a case where the beam center axis of the charged particle beam is moved due to state variation of the apparatus. When the beam center axis of a primary charged particle beam is adjusted with a deflector (aligner), a processing step (1) for measuring the sensitivity of the aligner and a processing step (2) for detecting the deviation between the center of the primary charged particle beam and the center of the objective aperture are provided. The charged particle beam apparatus has means for determining the aligner set values, using the aligner sensitivity measured in the processing step (1) and the amount of deviation detected in the processing step (2), such that the primary charged particle beam passes through the center of the objective aperture and controlling the aligner using the aligner set values.