Pump-probe technique enables to capture short-lived photo-excited molecule. Herein, pump-probe single crystal X-ray structure analysis about a photo-excited organic photocatalyst is described. Owing to atomic-resolved observation by single crystal X-ray structure analysis, three-dimensional geometrical feature of a target photocatalyst at a photo-excited state revealed in detail. Effects of steric hindrances and intermolecular interactions in a crystal on photoinduced geometrical change were also clarified. Those ensure the electronic feature of the target photocatalyst in action and elucidate a long-lived character of its photo-excited state.