Metal–organic frameworks (MOFs) have received much attention as a solid‐state electrolyte in proton exchange membrane fuel cells. The introduction of proton carriers and functional groups into MOFs can improve the proton conductivity attributed to the formation of hydrogen‐bonding networks, while the underlying synergistic mechanism is still unclear. Here, a series of flexible MOFs (MIL‐88B, [Fe3O(OH)(H2O)2(O2C‐C6H4‐CO2)3] with imidazole) is designed to modify the hydrogen‐bonding networks and investigate the resulting proton‐conducting characteristics by controlling the breathing behaviors. The breathing behavior is tuned by varying the amount of adsorbed imidazole into pore (small breathing (SB) and large breathing (LB)) and introducing functional groups onto ligands (‐NH2, ‐SO3H), resulting in four kinds of imidazole‐loaded MOFs−Im@MIL‐88B‐SB, Im@MIL‐88B‐LB, Im@MIL‐88B‐NH2, and Im@MIL‐88B‐SO3H. Im@MIL‐88B‐LB without functional groups exhibits the highest proton conductivity of 8.93 × 10−2 S cm−1 at 60 °C and 95% relative humidity among imidazole‐loaded proton conductors despite the mild condition, indicating that functional groups may not be always required to enhance proton conductivity. The elaborately controlled pore size and host–guest interaction in flexible MOFs through imidazole‐dependent structural transformation are translated into the high proton concentration without the limitation of proton mobility, contributing to the formation of effective hydrogen‐bonding networks in imidazole conducting media.

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