The growth of complex organic macromolecular materials in solution is a pervasive phenomenon in both natural and synthetic systems, yet the underlying growth mechanisms remain largely unresolved. Using liquid-phase transmission electron microscopy (TEM), we elucidate the real-time growth pathways of covalent organic framework (COF) onion nanostructures, which involve graphitic layer formation, subsequent layer attachment, onion ring closure, and structural relaxation. This process is marked by variations in orientation and curvature, driven by the dynamic formation of the COF structure, which further regulates order-disorder transition and defect generation within the framework. Our in situ TEM characterizations provide valuable insights into how molecular arrangement drives the formation of complex nanostructures. We anticipate that direct imaging of COF nanostructure growth in liquids will open new opportunities for controlling COF crystal morphology, composition, and hierarchical structure development.