There is provided an ion milling apparatus and sample holder permitting one to observe a sample, which has been milled, with an electron microscope without transferring the sample to a different holding member. The ion milling apparatus has an ion source, a sample holder, and a sample stage. The sample holder includes: a holder body having a sample holding portion for holding the sample; and a cover member detachably mounted to the holder body and hermetically sealing the sample held on the sample holding portion. The holder body has a shield plate and a field-correcting plate for correcting electric fields around the sample held on the sample holding portion.