An electron microscope has a large depth of focus in comparison with an optical microscope. Thus, information is superimposed on one image in the direction of depth. Therefore, it is necessary to accurately specify the three-dimensional position and density of a structure in a specimen so as to observe the three-dimensional structure of the interior of the specimen by using the electron microscope. Furthermore, a specimen that is observed with the optical microscope on a slide glass is not put into a TEM device of the related art. Thus, performing three-dimensional internal structure observation with the electron microscope on a location that is observed with the optical microscope requires very cumbersome preparation of the specimen. By controlling a vector parameter that defines the interrelationship between a primary charged particle beam and the specimen and by irradiation with the primary charged particle beam with a plurality of different vector parameters, images of transmitted charged particles of the specimen that correspond to each of the vector parameters are obtained. Irradiation with the primary charged particle beam is performed on the specimen that is arranged either directly or through a predetermined member on a detector which detects charged particles transmitted through or scattered by the interior of the specimen.