In a sample height regulating method, an area including the observation point on the sample is scan-irradiated with a first charged particle beam to obtain a first secondary electron image including the observation point. An area including the observation point on the sample is then scan-irradiated with a second charged particle beam to obtain a second secondary electron image including the observation point. Thereafter, based on magnifications of the first secondary electron image and the second secondary electron image and a distance between the observation point in the first secondary electron image and the observation point in the second secondary electron image, a height of the sample required for focusing the first charged particle beam and the second charged particle beam on the observation point is calculated. A sample stage supporting the sample is then displaced so as to position the sample at the calculated sample height.