Developing solid-state electrolytes with high proton conductivity for use in proton exchange membranes fuel cells remains a challenge. Metal-organic frameworks (MOFs), which display high surface areas, functional pore surface, and rich structural tunability, have received considerable attention as a new candidate for a solid-state proton conductor. The encapsulation of proton carriers into the pore spaces of MOFs is a widely used strategy to enhance their proton conductivity attributed to the formation of hydrogen-bonding networks on which the influence of the guest molecules has largely been unexplored. In this study, we synthesized imidazole molecules-loaded flexible MOFs (IM@Fe-MIL-88B) and investigated its effect on proton conduction by controlling the breathing effect, which possibly provides the formation of successive proton conduction pathway. The breathing behaviors of flexible IM@Fe-MIL-88B are tuned through varying the accommodated amount of imidazole and substituting functional groups onto MOF linkers. The delicately designed strong host-guest interaction can induce selectively imidazole-dependent structural transformation which leads to a full breathing effect on the framework, contributing to efficient proton conduction due to high concentration of proton carriers and the formation of dense and stable hydrogen bonding networks. To the best of our knowledge, IM@Fe-MIL-88B possesses the highest proton conductivity with the value of 8.93×10-2 S cm-1 at 95% RH and 60 °C among the imidazole loaded proton conducting materials. Our study provides the promise of the design of hydrogen-bonding networks for the exploration of solid-state proton conductors.