Photosensitive lanthanide‐based single‐molecule magnets (Ln−SMM) are very attractive for their potential applications in information storage, switching, and sensors. However, the light‐driven structural transformation in Ln−SMMs hardly changes the coordination number of the lanthanide ion. Herein, for the first time it is reported that X‐ray (λ=0.71073 Å) irradiation can break the coordination bond of Dy−OH2 in the three‐dimensional (3D) metal‐organic framework Dy2(amp2H2)3(H2O)6 ⋅ 4H2O (MDAF‐5), in which the {Dy2(OPO)2} dimers are cross‐linked by dianthracene‐phosphonate ligands. The structural transformation proceeds in a single‐crystal‐to‐single‐crystal (SC‐SC) fashion, forming the new phase Dy2(amp2H2)3(H2O)4 ⋅ 4H2O (MDAF‐5‐X). The phase transition is accompanied by a significant change in magnetic properties due to the alteration in coordination geometry of the DyIII ion from a distorted pentagonal bipyramid in MDAF‐5 to a distorted octahedron in MDAF‐5‐X.