A system of polar ordered resins was established for purification of chlorogenic acid in Flos Lonicerae. It was composed of three reversed phase resins, AB-8, DM-130 and NKA-9, representative for their gradually increased polarity and selectivity. A method of RP-HPLC was used for determination of chlorogenic acid. And the performance of adsorption and desorption for chlorogenic acid with the system of polar ordered resins was studied. Furthermore, the effects of concentration, pH and flow rate of the adsorbate on adsorption ability were researched. It is indicated that the optimum parameters for chlorogenic acid are as follows:pH 3.5 with a flow rate of 2.5 BV/h, the concentration of extract solution at 0.50, 0.40, 0.30 g/L respectively for the adsorptive operation twice, and 6.93, 8.66, 10.39 mol/L ethanol used as gradient eluants. The purity of resulted product of chlorogenic acid arrives 70.20% with yield of 89.79%. With simple procedures, low costs and high purity product, the method of system of polar ordered resins followed by sequential reversed phase separations can be used to refine the chlorogenic acid in the extraction of Flos Lonicerae.