Understanding the spatial distribution and different nature of active sites and elucidating their synergy in heterogeneous catalysts are fundamentally important for providing comprehensive insight into relevant structure–function relationships. However, this is difficult to achieve in microporous zeolite materials owing to the nearly indistinguishable physicochemical properties of each acidic site observed by conventional techniques. Here we report the real-space observation, with atomic molecular insights, of fascinating acidic properties in dual-pore channels of mordenite (H-MOR) zeolite using a combination of nuclear magnetic resonance probe molecule techniques and density functional theory calculations. Accordingly, the impact of acidic properties (e.g., detailed acidic distribution, pore confinement effect, and synergy effect of Brønsted acid pairs) of H-MOR zeolite on catalytic performance has been clarified. These results offer new insights into cooperative acid-catalyzed reactions over porous acidic catalysts with diverse pore architectures.