The development of novel stationary phases with specific functionality is of great importance in chromatographic separation. Herein, we fabricated fluoro-functionalized spherical covalent organic frameworks (SF-COFs) via a bottom-up strategy as stationary phases for high-performance liquid chromatography (HPLC). Benefiting from the significant monodispersity, narrow size distribution, and high fluorine content, the SF-COFs packed column showed high column efficiency and excellent resolution for the separation of the organic fluorides involving polyfluorobenzenes, polychlorobenzenes, polybromobenzenes, perfluoroalkyl methacrylates, and halogenated trifluorotoluenes, which cannot be separated on the fluorine-free spherical covalent organic frameworks packed column. Especially, the column efficiency of 20 100-38 500 plates/m was obtained for polyfluorobenzenes, and the relative standard deviations of the retention time for continuous 10 separations of polychlorobenzenes and polybromobenzenes were less than 0.98%. Furthermore, the prepared SF-COFs packed column showed overwhelming superiority in the separation of organic halides compared with commercial C18 and pentafluorophenyl (PFP) packed columns. In addition, the compounds with different hydrophobicity or aromatic ring structure were also successfully separated on the SF-COFs packed column. This work extended the application of spherical COFs and provided a new way to introduce specific functional groups into the COF-based stationary phase for HPLC.