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Herein, we report an efficient separation and enrichment method for chlorogenic acid from crude extracts of Eucommia ulmoides leaves using carbon adsorbents. The effects of the pore structure of the carbon adsorbents on the adsorption capacity were studied. Of the four adsorbents investigated, mesoporous carbon (MC3) showed the highest adsorption capacity (294 mg/g of carbon) for chlorogenic acid due to its high mesopore volume. The static adsorption of CGA on carbon can be accurately described using the Freundlich equation. The kinetics of adsorption follow a pseudo-second-order process. External mass transfer was the controlling step of the adsorption process. Dynamic adsorption on MC3 demonstrated that chlorogenic acid began to break through after 28 bed volumes of extract was loaded. This mesoporous carbon-treatment procedure is safe, economic and has the potential to be scaled up for commercial application.