Fluorinated porous materials, which can provide specific fluorine-fluorine interaction, hold great promise for fluoride analysis. Here, a novel fluorinated covalent-organic polymer was prepared by using 2,4,6-tris(4-aminophenyl)-1,3,5-triazine and 2,3,5,6-tetrafluorotelephtal aldehyde as the precursors and introduced as stationary phase for open-tubular capillary electrochromatography. The as-synthesized fluorinated covalent-organic polymer and the modified capillary column were characterized by infrared spectroscopy, scanning electron microscopy, and energy dispersive X-ray spectrometry. Based on strong hydrophobic interaction and fluorine-fluorine interaction provided by fluorinated covalent-organic polymer coating layer, the modified column showed powerful separation selectivity toward hydrophobic compounds, organic fluorides, and fluorinated pesticides. Additionally, the fluorinated covalent-organic polymer with good porosity and regular shape was uniformly and tightly coated on the capillary inner wall. The obtained highest column efficiency could reach up to 1.2 × 10 5 plates⋅m −1 for fluorophenol. The loading capacity of the modified column can reach 141 pmol for trifluorotoluene. Besides, the relative standard deviations of retention times for intraday run (n = 5), interday run (n = 3), and between columns (n = 3) were all less than 2.55%. Significantly, this novel fluorinated material-based stationary phase shows great application potential in fluorides analysis.