The combination of alternate recycling and direct recycling preparative liquid chromatography method was developed for the isolation of chemical constituents from Ziziphora clinopodioides Lam. The crude extract was obtained from Ziziphora clinopodioides Lam. by solvent extraction, column chromatography and reversed-phase (RP) flash chromatography. All the separations were performed with methanol and water as mobile phases and the developed recycling preparative method was used with twin RP columns switched by a two-position ten-way valve for the separation. The mobile phase was recycled in close loop with a two-position six-way valve. The fraction I and fraction II from reversed-phase flash chromatography were selected for the demonstration of separation power of the proposed protocol, and five compounds were obtained from Ziziphora clinopodioides Lam. The isolated five compounds were identified as pinocembrin-7-O-rutinoside, pinocembrin-7-O-rutinoside, acacetin-7-O-rutinoside, picein and protocatechuic acid with nuclear magnetic resonance (NMR). The experimental results showed that the developed preparation method exhibited higher separation efficiency with less mobile phase used than the reported methods, and could be expected as an effective method for the separation of complex natural products, especially the compounds with similar structures.