A sufficient processing speed and sufficient processing accuracy are obtained in a microstructure manufacturing method using ion beams. The microstructure manufacturing method includes the steps of: (a) irradiating a first region of a sample with a first ion beam (projection ion beam) formed by being passed through a first opening portion of a first mask, and etching the sample; and (b) irradiating a second region that is wider than the first region in a direction along a beam width, with a second ion beam (projection ion beam), and processing the sample. Furthermore, a magnitude of a skirt width of a longitudinal section of the second ion beam is smaller than a magnitude of a skirt width of a longitudinal section of the first ion beam.