Morphological control of covalent organic frameworks (COFs) is particularly interesting to boost their applications; however, it remains a grand challenge to prepare hollow structured COFs (HCOFs) with high crystallinity and uniform morphology. Herein, we report a versatile and efficient strategy of amorphous-to-crystalline transformation for the general and controllable fabrication of highly crystalline HCOFs. These HCOFs exhibited ultrahigh surface areas, radially oriented nanopore channels, quite uniform morphologies, and tunable particle sizes. Mechanistic studies revealed that H2O, acetic acid, and solvent played a crucial role in manipulating the hollowing process and crystallization process by regulating the dynamic imine exchange reaction. Our approach was demonstrated to be applicable to various amines and aldehydes, producing up to 10 kinds of HCOFs. Importantly, based on this methodology, we even constructed a library of unprecedented HCOFs including HCOFs with different pore structures, bowl-like HCOFs, cross-wrinkled COF nanocapsules, grain-assembled HCOFs, and hydrangea-like HCOFs. This strategy was also successfully applied to the fabrication of COF-based yolk-shell nanostructures with various functional interior cores. Furthermore, catalytically active metal nanoparticles were implanted into the hollow cavities of HCOFs with tunable pore diameters, forming attractive size-selective nanoreactors. The obtained metal@HCOFs catalysts showed enhanced catalytic activity and outstanding size-selectivity in hydrogenation of nitroarenes. This work highlights the significance of nucleation-growth kinetics of COFs in tuning their morphologies, structures, and applications.