Thus far, numerous new stationary phases have been developed. A fluorine-containing embedded carbon dots (F3-CDs-SiO 2 ) stationary phase was first designed and synthesized. The resulting F3-CDs-SiO 2 stationary phase was characterized carefully by scanning electron microscopy, transmission electron microscopy, elemental analysis, X-ray photoelectron spectroscopy, and Brunauer−Emmett−Teller experiment. The F3-CDs-SiO 2 stationary phase was slurry packed into the HPLC column (150 × 2.1 mm) for evaluation. Furthermore, the F3-CDs-SiO 2 column was successfully used for separation of pesticides, nucleosides, sulfonamides, alkaloids, and alkylbenzenes. The retention mechanism (including hydrophobic interaction, F−F, hydrogen bond interaction, ion-exchange, dipole− dipole interaction, electrostatic interaction, etc.) was investigated carefully. Meanwhile, the F3-SiO 2 stationary phase was synthesized and used to evaluate the role of CDs. Furthermore, various commercial stationary phases (including amino-SiO 2 , diol-SiO 2 , C18-SiO 2 , and PFP-SiO 2 ) were used for comparison. Moreover, the F3-CDs-SiO 2 column possessed good repeatability, reproducibility, and stability in separation of versatile analytes.