An effective high-speed counter-current chromatography method was established for the preparative isolation and purification of two phenylpropanoid glycosides from the Tibetan medicinal plant Pedicularis longiflora Rudolph. var. tubiformis (Klotz). Tsoong. With a two-phase solvent system composed of chloroform-n-butanol-methanol-water (4:3:4:5, v/v), 40 mg of an extract of Pedicularis longiflora Rudolph. var. tubiformis (Klotz). Tsoong was separated to yield 20 mg of verbascoside and 18 mg of isoacteoside, with purity values of 97 and 98%, respectively. The chemical structures of these two components were identified by proton and carbon nuclear magnetic resonance. In addition, the antioxidant activity of the two phenylpropanoid glycosides was evaluated by 2,2-diphenyl-1-picrylhydrazyl (DPPH)-high-performance liquid chromatography, and the results showed that the two components exhibited strong antioxidant DPPH radical scavenging activity, with IC50 values of 15.6 and 18.9 µg/mL, respectively.