Preparative parallel high performance liquid chromatography combined with solvent partition and other pretreatments were adopted to separate and purify compounds from an extract of Scutellaria barbata D. Don. Mass-triggered fraction collection allowed the rapid and precise isolation of target compounds. Twelve compounds were isolated from the extract of S. barbata D. Don, their purity in area percent was determined by HPLC analysis, and the structures of seven compounds were further identified with HPLC/ESI-MS, (1)H NMR, and( 13)C NMR, among which 4-(3,4-dihydroxy-phenyl)-but-3-en-2-one, acacetin-7-diglucuronide, and luteolin-7-diglucuronide were the first to be identified from this plant. The results demonstrated that multi-channel parallel preparative HPLC/UV/MS is an efficient method for isolation and purification of compounds from natural products.