The present invention provides a technology for avoiding radiation of an ion beam at a position other than a desired processing position. A microstructure manufacturing method includes a step of radiating an ion beam to a sample; a step of supplying a gas to the sample; a step of stopping supplying the gas to the sample; and a step of stopping radiating the ion beam to the sample. The step of radiating the ion beam is performed earlier than the step of supplying the gas or the step of stopping supplying the gas is performed earlier than the step of stopping radiating the ion beam.