Metal-organic framework (MOF) heterostructures have shown promising applications in gas adsorption, gas separation, catalysis, and energy, arising from the synergistic effect of each component. However, owing to the difficulty in controlling the size, shape, nucleation, and growth of MOFs, it remains a great challenge to construct MOF heterostructures with precisely controlled orientation, morphology, dimensionality, and spatial distribution of each component. Here, we report a seeded epitaxial growth method to prepare a series of hierarchical MOF heterostructures by engineering the structures, sizes, dimensionalities, morphologies, and lattice parameters of both MOF seeds and the secondary MOFs. In these heterostructures, PCN-222 (also known as MOF-545) nanorods selectively grow along the major axis of the ellipsoid-like PCN-608 nanoparticles, on the two end facets of the hexagonal prism-like NU-1000 nanorods, and on the two basal planes of the hexagonal PCN-134 nanoplates, while Zr-BTB nanosheets selectively grow on the six edge facets of PCN-134 nanoplates. The selective epitaxial growth of MOFs opens the way to synthesize different hierarchical heterostructures with tunable architectures and dimensionalities, which could process various promising applications.