A new and efficient hydrophilicity-directed approach (HDA) is developed to encapsulate large guest molecules beyond the aperture size limitation in the nanospace of metal-organic frameworks (MOFs), as exemplified by the self-assembly of a metal organic polyhedral (MOP) M6L4 into MIL-101. This strategy is based on the different hydrophilicities between inner and outer surfaces of the preformed MOF that may direct the self-assembly of the MOP in the MOF pores by using a two-solvent system. Importantly, as the MOP guest molecule is larger than the MOF aperture size, aggregation and leaching are effectively prevented, endowing the encapsulated MOP with significantly enhanced reactivity and stability in the catalytic transformations as compared to the pristine MOP.