We demonstrate the realization of hierarchically organized MOF (metal-organic framework) multilayer systems with pronounced differences in the size of the nanoscale pores. Unusually large values for the lattice constant mismatch at the MOF-MOF heterojunctions are made possible by a particular liquid-phase epitaxy process. The multiheteroepitaxy is demonstrated for the isoreticular SURMOF-2 series [ Liu et al. Sci. Rep. 2012 , 2 , 921 ] by fabricating trilayer systems with lattice constants of 1.12, 1.34, and 1.55 nm. Despite these large (20%) lattice mismatches, highly crystalline, oriented multilayers were obtained. A thorough theoretical analysis of the MOF-on-MOF heterojunction structure and energetics allows us to identify the two main reasons for this unexpected tolerance of large lattice mismatch: the healing of vacancies with acetate groups and the low elastic constant of MOF materials.