Crystal size effect is of vital importance in materials science by exerting significant influence on various properties of materials and furthermore their functions. Crystal size effect of covalent organic frameworks (COFs) has never been reported because their controllable synthesis is difficult, despite their promising properties have been exhibited in many aspects. Here, we report the diverse crystal size effects of two representative COFs based on the successful realization of crystal-size-controlled synthesis. For LZU-111 with rigid spiral channels, size effect reflects in pore surface area by influencing the pore integrity, while for flexible COF-300 with straight channels, crystal size controls structural flexibility by altering the number of repeating units, which eventually changes sorption selectivity. With the understanding and insight of the structure-property correlation not only at microscale but also at mesoscale for COFs, this research will push the COF field step forward to a significant advancement in practical applications.