The capability to build up stable, switchable catalysts for complex artificial systems that can mimic the responsiveness of biological systems to multiple triggers is highly desirable and challenging. Herein, we engineer such a system by physically locking catalytically active metal clusters (MCs) inside individual cationic molecular organic cages (I-Cages), where the responsive and task-specific counteranions of I-Cages impart MCs with a programmable gating effect. This allows for precise spatial and temporal control over chemical reactions by regulating accessibility of reagents to the MC sites. Following this strategy, we have successfully tailored catalytic activity of a series of model catalysis (e.g., methanolysis of ammonia borane, and the reduction of 4-nitroaniline) by employing light and pH stimuli, as well as their combination, for programmable-activity control.