Natural photosynthetic systems require spatiotemporal organization to optimize photosensitized reactions and maintain overall efficiency, involving the hierarchical self-assembly of photosynthetic components and their stabilization through synergistic interactions. However, replicating this level of organization is challenging due to the difficulty in efficiently communicating supramolecular nano-assemblies with nanoparticles or biological architectures, owing to their dynamic instability. Herein, we demonstrate that the supramolecular reconstruction of self-assembled amphiphilic rhodamine B nanospheres (RN) through treatment with metal-phenolic coordination complexes results in the formation of a stable hybrid structure. This reconstructed structure enhances electron transfer efficiency, leading to improved photocatalytic performance. Due to the photoluminescence quenching property of RN and its electronic synergy with tannic acid (T) and zirconium (Z), the supramolecular complexes of hybrid nanospheres (RNTxZy) with Pt nanoparticles or a biological workhorse, Shewanella oneidensis MR-1, showed marked improvement in photocatalytic hydrogen production. The supramolecular hybrid particles with a metal-phenolic coordination layer showed 5.6- and 4.0-fold increases, respectively, in the productivities of hydrogen evolution catalyzed by Pt (Pt/RNTxZy) and MR-1 (M/RNTxZy), respectively. These results highlight the potential for further advancements in the structural and photochemical control of supramolecular nanomaterials for energy harvesting and bio-hybrid systems.