A four-channel preparative HPLC was employed to isolate and purify compounds from licorice extract. Two separation modes, RP and hydrophilic interaction LC (HILIC), were used in preparative HPLC. HILIC mode was adopted to resolve the purification of the compounds with similar hydrophobicity, which were co-eluted under RP mode. Using the two separation modes during the purification process, fifteen compounds were isolated from licorice extract. The results indicated that preparative HPLC performed under HILIC mode is an efficient method for the isolation and purification of compounds from natural products.