The dynamic behaviour of metal‐ligand bonding cultivates stimuli‐mediated structural transformations in self‐assembled molecular architectures. The propensity of synthetically designed self‐assembled systems to interchange between higher‐order architectures is increased multi‐fold when the building blocks have higher conformational degrees of freedom. Herein, we report a new ligand, (2,7‐bis(di(pyridin‐4‐yl)amino)‐9H‐fluoren‐9‐one) (L), which, upon self‐assembly with a cis‐[(ethylene‐1,2‐diamine)Pd(NO3)2] acceptor (M), resulted in the formation of a M6L3 trifacial barrel (C1) in water. Interestingly, during crystallization, a rare M12L6 triangular orthobicupola architecture (C2) was generated along with C1. C2 could also be generated in solution via the application of several stimuli. C1 in aqueous medium could stabilize one trans‐stilbene (tS) or cis‐stilbene (cS) molecule in its cavity, with a selectivity for the former from their mixture. Moreover, C1 acted as an effective host to prevent the otherwise facile photoisomerization of tS to cS inside its hydrophobic cavity under UV irradiation. Conversely, the visible‐light‐induced reverse isomerization of encapsulated cS to encapsulated tS could be achieved readily due to the better stabilization of tS within the cavity of C1 and its transparency to visible light. A multi‐functional system was therefore designed, which at the same time is stimuli‐responsive, shows isomer selectivity, and photo‐protects trans‐stilbene.