Mesocrystals-superstructures of crystalline nanoparticles that are aligned in a crystallographic fashion-are of increasing interest for formation of inorganic materials with complex and sophisticated morphologies to tailor properties without changing chemical composition. Here we report morphogenesis of a novel mesocrystal consisting of nanoscale metal-organic frameworks (MOF) by using double hydrophilic block copolymer (DHBC) as a crystal modulator. DHBC selectively prefers the metastable hexagonal kinetic polymorph and promotes anisotropic crystal growth to generate hexagonal rod mesocrystals via oriented attachment and mesoscale assembly. The metastable nature of hexagonal mesocrystals enables further hierarchical morphogenesis by a solvent-mediated polymorphic transformation toward stable tetragonal mesocrystals that retain the outer hexagonal particle morphology. Furthermore, synthesis of hybrid MOFs, where hexagonal mesocrystals are vertically aligned on specific surfaces of cubic MOFs, is demonstrated. The present strategy opens a new avenue to create MOF mesocrystals and their hybrids with controlled size and morphology that can be designed for various potential applications.