Due to the general incompleteness of photochemical reactions, the photostationary structure in traditional photo-controlled host–guest self-assembly transfer is usually disordered or irregular. This fact readily affects the photoregulation or improvement of related material properties. Herein, a photoexcitation-induced aggregation molecule, hydroxyl hexa-(arylthio) benzene (HB), was grafted into β-cyclodextrin to form a far-from-equilibrium host–guest system. Upon irradiation, the excited state conformational change of HB can drive an order-to-order phase transition of the system, enabling a transfer of the initial linear nanostructure to a photostationary worm-like nanostructure with orderliness and crystallinity capability. Along with the photoexcitation-controlled phase transition, afterglow effect was obtained from the films prepared by doping the host–guest system into poly(vinyl alcohol). The afterglow effect had a superior water resistance, which successfully overcame the general sensitivity of doped materials with afterglow effect to water vapor. These results are expected to provide new insights for pushing forward chemical self-assembly from the light perspective, towards materials with superior and stable properties under light treatment.