Framework crystallization is an unresolved challenge in the chemistry of covalent organic frameworks (COFs) due to the poorly controlled simultaneous polymerization and crystallization processes. Here, we report the first morphogenesis of COF mesocrystals with two-dimensional hexagonal p6m symmetry through the combination of alkyl amine as a dynamic modulator and 2,4,6-triformylresorcinol imine as an asymmetrical building block. The amine modulator depresses the lateral growth of 2D sheets, and the slow kinetics combined with the asymmetrical conformation of 2,4,6-triformylresorcinol imine lead to the formation of transient imine macrocycles, which further undergo mesoscale self-assembly into nanotubular structures. The nanotubular structures tend to join together into rod-like bundles with ordered hexagonal rods, which finally grow into uniform hexagonal COF mesocrystals. The present strategy opens a nonclassical nucleation and crystal growth approach to create COFs with unexplored mesocrystal structures, which further extends the scope of crystalline framework materials and provides a new strategy for crystal morphogenesis. (C) 2020 Elsevier Inc. All rights reserved.