In this paper, we investigated the analytical potential of the use of single-walled carbon nanotubes (SWNTs) with different dispersion as additives in MEEKC. The addition of surfactant-coated single-walled carbon nanotubes (SC-SWNTs) in microemulsion provided a more efficient method than carboxylic SWNTs for the separation of three flavonoids and six phenolic acids depending on the interaction between the analytes and SWNTs surface. Additionally, the effect of important factors was examined by changing experimental variables such as the dispersion of SWNTs, surfactants and cosurfactants. Finally, the MEEKC method using SC-SWNTs was successfully applied to complex natural products (drug pair of Radix Astragali and Radix et Rhizoma Salvia Miltiorrhizae), with satisfactory results.