Understanding and control of the spatiotemporal stimuli-responsiveness of flexible metal-organic frameworks are crucial for the development of novel adsorbents for gas storage and separation technologies. Herein, we report two isostructural pillared-layer dynamic frameworks differing only in one atom that bridge a benzenocarboxylate linker. Through a synthetic approach, we switch the stepwise CO₂-induced transformation into a continuous one. Our findings are proved by equilibrium and time-resolved in situ powder X-ray diffraction collected during CO₂ adsorption at 195 K. Finally, we use high-pressure single and multi-gas adsorption experiments to show the superiority of continuous breathing in CH₄ storage and CH₄/CO₂ separation at 298 K. This report demonstrates that the desirable mechanism of flexible frameworks can be readily achieved through single-atom exchange enabling efficient gas separation and storage.