A proton-conducting metal–organic framework (MOF), {[Cu4(dpdo)12][H(H2O)27(CH3CN)12][PW12O40]3}n (where dpdo is 4,4′-bipyridine-N,N′-dioxide) (1), was synthesized by the reaction of CuHPW12O40·nH2O and dpdo at room temperature. Single-crystal X-ray diffraction analysis at 293 K revealed that 1 crystallized in the cubic space group Im-3 and presented a non-interwoven 3-D framework with cubic cavities and guest molecules. A large ionic water cluster H+(H2O)27, consisting of a water shell (H2O)26 and an encaged H+(H2O) as a center core, was trapped in the cubic cavity of the MOF {[Cu4(dpdo)12(PW12O40)3]−}∞. Thermogravimetric analysis suggests that 1 has high thermal stability, indicating that such a non-interwoven 3-D framework with cubic cavities is a suitable host for researching protonated water clusters. Its water vapor adsorption isotherm at room temperature and pressure shows that the water vapor adsorbed in it was 65.1 cm3 g−1 at the maximum allowable humidity. It exhibits good proton conductivities of 10−5–10−4 S cm−1 at 100 °C in the relative humidity range 35–98%.