The energy landscape of a supramolecular material can include different molecular packing configurations that differ in stability and function. We report here on a thermally driven crystalline order transition in the landscape of supramolecular nanostructures formed by charged chromophore amphiphiles in salt-containing aqueous solutions. An irreversible transition was observed from a metastable to a stable crystal phase within the nanostructures. In the stable crystalline phase, the molecules end up organized in a short scroll morphology at high ionic strengths and as long helical ribbons at lower salt content. This is interpreted as the result of the competition between electrostatic repulsive forces and attractive molecular interactions. Only the stable phase forms charge-transfer excitons upon exposure to visible light as indicated by absorbance and fluorescence features, second-order harmonic generation microscopy, and femtosecond transient absorbance spectroscopy. Interestingly, the supramolecular reconfiguration to the stable crystalline phase nanostructures enhances photosensitization of a proton reduction catalyst for hydrogen production.