A scanning probe microscope system capable of identifying an element with atomic scale spatial resolution comprises: an X-ray irradiation means for irradiating a measurement object with high-brilliance monochromatic X-rays having a beam diameter smaller than 1 mm; a probe arranged to oppose to the measurement object; a processing means for detecting and processing a tunneling current through the probe; and a scanning probe microscope having an alignment means for relatively moving the measurement object, the probe, and the incident position of the high-brilliance monochromatic X-rays to the measurement object.