The crystal structure of thermoelectric rhenium silicide with an ordered arrangement of vacancies is investigated by utilizing spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM) combined with synchrotron X-ray diffraction and conventional transmission electron microscopy. By STEM Cs corrected imaging, we can clearly observe Si vacancies in rhenium silicide, which is impossible without Cs correction. In addition, significantly reduced contrast levels are noted in STEM images for particular Si sites near vacancies. From the STEM image simulation, the reduced contrast levels are concluded to be due to anomalously large local thermal vibration of these Si atoms. The crystal structure of rhenium silicide can be successfully refined by the synchrotron X-ray diffraction starting with the deduced structure model from the STEM images and the occurrence of large local thermal vibration can be qualitatively confirmed. Furthermore, we confirm the validity of the refined crystal structure of rhenium silicide by comparing experimental images with simulated image generating with the refined crystal structure parameters.