An ion milling apparatus includes a pair of shielding members sandwiching a sample, and an ion source configured to irradiate the sample with an ion beam. The ion milling apparatus is configured to be capable of irradiating the sample with the ion beam in a first mode of irradiating the sample with the ion beam via one shielding member and in a second mode of irradiating the sample with the ion beam via the other shielding member.