This work reports the interesting and unique cation‐exchange behaviors of the first indium‐bridged purely inorganic 3D framework based on high‐nuclearity polyoxoniobates as building units. Each nanoscale polyoxoniobate features a fascinating near‐icosahedral core–shell structure with six pairs of unique inorganic “molecular tweezers” that have changeable openings for binding different metal cations via ion‐exchanges and exhibit unusual selective metal‐uptake behaviors. Further, the material has high chemical stability so that can undergo single‐crystal‐to‐single‐crystal metal‐exchange processes to produce a dozen new crystals with high crystallinity. Based on these crystals and time‐dependent metal‐exchange experiments, we can visually reveal the detailed metal‐exchange interactions and mechanisms of the material at the atomic precision level. This work demonstrates a rare systematic and atomic‐level study on the ion‐exchange properties of nanoclusters, which is of significance for the exploration of cluster‐based ion‐exchange materials that are still to be developed.