In a method of measuring a thin film sample of irradiating an electron beam to a thin film sample, detecting a generated secondary electron and measuring a film thickness of the thin film sample by utilizing the secondary electron, it is provided that the film thickness is measured accurately, in a short period of time and easily even when a current amount of the irradiated electron beam is varied. An electron beam 2b is irradiated, and a generated secondary electron 4 is detected by a secondary electron detector 6. A calculated value constituted by an amount of a secondary electron detected at a film thickness measuring region and an amount of a secondary electron detected at a reference region is calculated by first calculating means 11. A film thickness of the film thickness measuring region can be calculated from a calibration data of a standard thin film sample and the calculated value calculated by a sample 5.