A series of MOF-based hierarchical porous material, namely IPD-mesoMOF-1˜9, based on nanoscale MOFs of MIL-100(Al, Fe, Cr, Sc and In), MIL-53(Al), HKUST-1, DUT-5, DUT-4, MIL-101(Cr), MIL-101NDC(Cr), MIL-101BPDC(Cr) and MIL-110 respectively, forming the permanent interparticle porosities by using close (or relatively close) packing, and preparation methods thereof. Modulated or functionalized IPD-mesoMOFs can be applied for gas adsorption and molecule separation (such as CH4- and CO2-adsorption, gasoline/diesel desulfurization and purification), catalyst loadings and molecular recognition/immobilization of biological macromolecules and enzymes.