A scanning transmission electron microscope equipped with an aberration corrector is capable of automatically aligning the position of a convergence aperture with the center of an optical axis irrespective of skill and experience of an operator. The scanning transmission electron microscope system includes an electron source; a condenser lens configured to converge an electron beam emitted from the electron source; a deflector configured to cause the electron beam to perform scanning on a sample; an aberration correction device configured to correct an aberration of the electron beam; a convergence aperture configured to determine a convergent angle of the electron beam; and a detector configured to detect electrons passing through or diffracted by the sample. The system acquires information on contrast of a Ronchigram formed by the electron beam passing through the sample, and determines a position of the convergence aperture on the basis of the information.