Although there are many publications related to technological or methodological developments of CEC, few focus on the analysis of natural products, especially phytochemical bioactive compounds. This review summarized the application of CEC in the analysis of phytochemical bioactive components, including flavonoids, nucleosides, steroids, lignans, quinones and coumarins, as well as fingerprint analysis of herbs. The strategies for optimization of CEC conditions and detection were also discussed.