Flexible metal–organic frameworks (MOFs) are highly attractive porous crystalline materials presenting structural changes when exposed to external stimuli, the mechanism of which is often difficult to glean, owing to their complex and dynamic nature. Herein, a flexible interpenetrated Zr‐MOF, NU‐1401, composed of rare 4‐connected Zr6 nodes and tetratopic naphthalenediimide (NDI)‐based carboxylate linkers, was designed. The intra‐framework pore opening deformation and inter‐framework motions, when subjected to different solvent molecules, were investigated by single‐crystal XRD. The distance and overlap angle between the stacked NDI pairs in the entangled structure could be finely tuned, and the interactions between NDI and solvent molecules led to solvochromism. Furthermore, the presence of electron‐deficient NDI units in the linker and acid sites on the node of the interpenetrated porous structure offered high density of adsorption sites for ammonia molecules, resulting in high uptake at low pressures.