A functionalized isoreticular metal organic framework material, F-IRMOF-3, having a quaternary ammonium group was prepared by fast precipitation and solvothermal method. The synthesized MOFs exhibited good catalytic performance in the synthesis of glycerol carbonate (GC) from glycerol and urea. F-IRMOF-3 having a larger alkyl chain structure and a more nucleophilic counter anion than the synthesized congeners, exhibited better reactivity in the synthesis of GC. The introduction of a ZnO defect into the F-IRMOF-3 structure by fast precipitation was more advantageous for the glycerolysis of urea than the conventional solvothermal method because of the incorporation of acid-base bifunctional active sites by the former method. The effects of reaction parameters such as temperature, reaction time, catalyst loading, and degree of vacuum on the reactivity were also investigated. The F-IRMOF-3 catalyst can be easily recovered and reused without considerable loss of its initial activity.