Synthesizing uniform functional covalent organic framework (COF) microspheres is the prerequisite of applying COFs as novel stationary phases for liquid chromatography. However, the synthesis of functionalized COF microspheres is challenging due to the difficulty in maintaining microspheric morphology when conferring functions. Here, a facile and universal "self-limited dynamic linker exchange" strategy is developed to achieve surface functionalization of uniform COF microspheres. Six different types of COF microspheres are constructed, showing the universality and superiority of the strategy. The library of COF microspheres' stationary phases can be further enriched on demand by varying different functional building blocks. The "self-limited dynamic linker exchange" is attributed to the result of a delicate balance of reaction thermodynamics and molecular diffusion energy barrier. As a demonstration, the chiral functional COF microspheres are used as stationary phases of chiral chromatography and realized effective enantioseparation.