Installing different chemical entities onto crystalline frameworks with well-defined spatial distributions represents a viable approach to achieve ordered and complex synthetic materials. Herein, a covalent organic framework (COF-305) is constructed from tetrakis(4-aminophenyl)methane and 2,3-dimethoxyterephthalaldehyde, which has the largest unit cell and asymmetric unit among known COFs. The ordered complexity of COF-305 is embodied by nine different stereoisomers of its constituents showing specific sequences on topologically equivalent sites, which can be attributed to its building blocks deviating from their intrinsically preferred simple packing geometries in their molecular crystals to adapt to the framework formation. The insight provided by COF-305 supplements the principle of covalent reticular design from the perspective of non-covalent interactions and opens opportunities for pursuing complex chemical sequences in molecular frameworks.