Environmentally triggered major phenomenological switching, including in shape, size, or curvature, is widely found in particles that occur in nature. We demonstrate a generic approach towards dynamically reconfiguring the shape of β-cyclodextrin(β-CD)-based particles to exploit the unique light-responsive behavior that can trigger "stimuli-responsive" controlled release of active molecules. In detail, solely enabled by their architecture, flakes and spheres comprising binary complexes formed between β-CD and antibacterial stilbenes molecule and/or azobenzene derivative underwent active reconfiguration, including reversible shape-shifting and bioactivity switching. Interestingly, these two particles (flakes and spheres) exhibited reversible and reproducible changes in their shape over repeated UV-vis irradiation cycles. The "stimuli-responsive" shape-shifting of nano-system regulated the switch of bioactivity in vitro and in vivo, inhibited biofilm formation, decreased bacterial motility, and disrupted the flagellar biosynthesis process. Overall, we developed a β-CD-based supramolecular assembly system related to the design and shape-adaptable properties of particles, providing a new paradigm on their prospective applications in nanomedicine/nanopesticide delivery.