The efficient purification method of high purity flavonoids from Hippophae rhamnoides L. (sea buckthorn) was reported. A series of adsorption resins with novel structure were synthesized on the basis of the Friedel-Crafts catalyzed and amination reaction. Functional groups, such as the chloromethyl or the amino group, were introduced into the resin matrix, respectively, to raise the specific surface area, produce the hydrogen-bonding interaction, and enhance the adsorption selectivity toward flavone compounds. The results showed that the adsorbent DDM-1 with 0.44 mmol/g chloromethyl groups and the adsorbent DDM-2 with 0.68 mmol/g amino groups performed high purity and adsorption to flavone compounds in Hippophae rhamnoides L. leaves, respectively, obviously higher than that from commercial adsorbents due to their more pores, higher surface area and pore size, and stronger hydrogen-bonding interaction between flavonoids and surface functional groups of the adsorbents, which maintained the adsorption driving force. The isotherms and kinetics of synthetic resins were also studied systematically. In order to get the optimal sample, the No. 3 and No. H were selected and used in the developed two-separation-step protocol due to their high adsorption and purity capacities, respectively. The purity of flavonoids after the two steps was increased 6.62-fold from 5.55% to 36.75%. The method showed its universality via good effects on the purification of flavonoids from Hippophae rhamnoides L. leaves.