X-ray induced atomic motion on a Ge(111)-c(2 x 8) clean surface at room temperature was directly observed with atomic resolution using a synchrotron radiation (SR)-based scanning tunneling microscope (STM) system under ultra high vacuum condition. The atomic motion was visualized as a tracking image by developing a method to merge the STM images before and after X-ray irradiation. Using the tracking image, the atomic mobility was found to be strongly affected by defects on the surface, but was not dependent on the incident X-ray energy, although it was clearly dependent on the photon density. The atomic motion can be attributed to surface diffusion, which might not be due to core-excitation accompanied with electronic transition, but a thermal effect by X-ray irradiation. The crystal surface structure was possible to break even at a lower photon density than the conventionally known barrier. These results can alert X-ray studies in the near future about sample damage during measurements, while suggesting the possibility of new applications. Also the obtained results show a new availability of the in-situ SR-STM system.