An analysis method using an electron microscope, detects by a first electronography detector an electron beam transmitted through or scattered by a sample to detect an ADF image of the sample, detects by a second electronography detector the electron beam passing through the first electronography detector to detect an MABF image, adjusts a focal point of the electron beam to be located on the film of the sample to obtain first and second electronographies by the second and first electronography detectors, respectively, adjusts the focal point of the electron beam to be located on the substrate of the sample to obtain third and fourth electronographies by the second and first electronography detectors, respectively, aligns positions of the second and fourth electronographies based on the first and third electronographies, and after the aligning, subtracts the fourth electronography from the second electronography to obtain an image of the film.