Resolving the detailed structures of metal organic frameworks is of great significance for understanding their structure-property relation. Real-space imaging methods could exhibit superiority in revealing not only the local structure but also the bulk symmetry of these complex porous materials, compared to reciprocal-space diffraction methods, despite the technical challenges. Here we apply a low-dose imaging technique to clearly resolve the atomic structures of building units in a metal-organic framework, MIL-125. An unexpected node structure is discovered by directly imaging the rotation of Ti-O nodes, different from the unrotated structure predicted by previous X-ray diffraction. The imaged structure and symmetry can be confirmed by the structural simulations and energy calculations. Then, the distribution of node rotation from the edge to the center of a MIL-125 particle is revealed by the image analysis of Ti-O rotation. The related defects and surface terminations in MIL-125 are also investigated in the real-space images. These results not only unraveled the node symmetry in MIL-125 with atomic resolution but also inspired further studies on discovering more unpredicted structural changes in other porous materials by real-space imaging methods.