1. A pattern inspection method comprising: measuring a pattern to be inspected, including: irradiating with a charged particle beam a first region of a surface of a sample having the pattern to be inspected formed therein, acquiring a first two-dimensional image showing a state of the surface of the sample by detecting at least one of a secondary charged particle, a reflection charged particle, and a back scattering charged particle emitted from the sample due to the irradiation of the first region with the charged particle beam, searching, within the first two-dimensional image, for a first pattern similar to a previously prepared reference image, and when the first pattern similar to the reference image is detected at a first place within the first two-dimensional image, focusing the charged particle beam at a second place that is different from the first place, acquiring a second two-dimensional image magnified higher than the first two-dimensional image at the first place; and further measuring the pattern to be inspected when the first pattern similar to the reference image is not detected in the first two-dimensional image, the further measuring including: irradiating with the charged particle beam a second region of the surface of the sample that has not been irradiated, acquiring a third two-dimensional image showing a state of the surface of the sample by detecting at least one of a secondary charged particle, a reflection charged particle, and a back scattering charged particle emitted from the sample due to the irradiation of the second region with the charged particle beam, searching, within the third two-dimensional image, for a second pattern similar to the reference image, when the second pattern similar to the reference image is detected at a third place within the third two-dimensional image, focusing the charged particle beam at a fourth place that is different from the third place, acquiring a fourth two-dimensional image magnified higher than the third two-dimensional image at the third place.