A charged particle beam apparatus facilitating adjusting a 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 first processing step for measuring the sensitivity of the aligner and a second processing step 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 determines the aligner set values, using the aligner sensitivity measured in the first processing step and the amount of deviation detected in the second processing step, such that the primary charged particle beam passes through the center of the objective aperture and controls the aligner using the aligner set values.