Provided is a composite charged particle beam apparatus, including: an electron beam column for irradiating a sample with an electron beam; an ion beam column for irradiating the sample with an ion beam to perform etching processing; a sample stage drive portion for moving a sample stage in an irradiation axis direction of the electron beam; and a column adjusting portion for moving the ion beam column relatively to a sample chamber such that the sample is irradiated with the ion beam at a position irradiated with the electron beam.