Abstract A facile, in situ growth strategy for the synthesis of monodispersed COF@SiO 2 microspheres is reported. The microspheres have uniform and controllable COF shells, and are used as the stationary phase for HPLC. The TpBD COF, constructed from 1,3,5‐triformylphloroglucinol (Tp) and benzidine (BD), is taken as the COF shell, and aminosilica (SiO 2 −NH 2 ) is employed as the core to support the TpBD shell. The TpBD shell thickness is adjusted by controlling the concentrations of the Tp and BD monomers. The TpBD@SiO 2 packed columns show excellent hydrophobic selectivity, and good reproducibility for the separation of neutral (toluene and ethylbenzene, polycyclic aromatic hydrocarbons), acidic (hydroquinone, p ‐cresol, and p ‐chlorophenol), and basic molecules (nucleobases, nucleosides, and deoxynucleosides).