An ion beam processing apparatus includes an ion beam irradiation optical system that irradiate a rectangular ion beam to a sample held on a first sample stage, an electron beam irradiation optical system that irradiates an electron beam to the sample, and a second sample stage on which a test piece, extracted from the sample by a probe, is mounted. An angle of irradiation of the ion beam can be tilted by rotating the second sample stage about a tilting axis. A controller controls the width of skew of an intensity profile representing an edge of the rectangular ion beam in a direction perpendicular to a first direction in which the tilting axis of the second sample stage is projected on the second sample stage surface so that the width will be smaller than the width of skew of an intensity profile representing another edge of the ion beam in a direction parallel to the first direction.