A new multifunctional ionic liquid-based metal-organic hybrid (PMAIL) was synthesized by anion exchange between as-synthesized phosphonate-based ionic liquid and phosphomolybdic acid and applied to epoxy resin (EP) as an efficient flame retardant. As expected, with only 1 wt% addition of PMAIL, the char yield of EP-PMAIL1 composite at 700 degrees C was significantly improved by 108.3% from 12.0% for neat epoxy resin to 25.0%, demonstrating the outstanding catalytic charring effect of PMAIL. Meanwhile, EP-PMAIL6 composite (6 wt% addition) can reach V-0 rating in the UL-94 vertical burning tests easily, and its peak heat release rate and total smoke production of EP-PMAIL6 were dropped by 31.0 and 15.4%, respectively, compared with neat EP. Moreover, the results from cone calorimetry tests showed that the char yield of EP-PMAIL6 was enhanced by 162% from 9.5 to 24.9% compared with neat EP, resulting in a strong intumescent char layer structure with outstanding fire retardance and mechanical properties. The thermo-oxidative stable protective layer retarded the transfer of heat and flammable volatiles during combustion and protected the epoxy matrix from further degradation. In conclusion, our results might provide a new perspective for producing composites with excellent flame retardancy and smoke suppression properties using ionic liquid-based metal-organic hybrid.