A charged particle microscope apparatus includes a radiation optical system that radiates a focused charged particle beam to an upper side of a sample provided with a pattern and scans the sample; a detection optical system that detects charged particles generated from the sample to which the charged particle beam has been radiated by the radiation optical system; and a processing unit that processes the charged particles detected by the detection optical system to obtain a charged particle image of the sample, estimates diffusion of the charged particles at any depth of the pattern of the sample, on the basis of information on a depth or a material of the pattern of the sample or radiation energy of the charged particle beam in the radiation optical system; corrects the obtained charged particle image using the estimated diffusion of the charged particles; and processes the corrected charged particle image.