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The invention relates to a preparation method for separating high-purity hispidulin and nepetin from common sage herb by high-speed countercurrent chromatography. The preparation method comprises the following steps of: (1) preparing a proper solvent system and standing to laminate so as to obtain an upper phase and a lower phase; (2) selecting the upper phase as a stationary phase and the lower phase as a mobile phase, filling the fixed phase into a countercurrent chromatograph column, adjusting the rotating speed of a host to be 600 to 1,000 rpm, pumping the mobile phase into the column at the flow velocity of 0.5 to 5.0 ml/min, and performing sample introduction by a sample valve after the whole system establishes dynamic balance; and (3) receiving target components according to a detector ultraviolet spectra, concentrating and crystallizing to obtain the high-purity hispidulin and nepetin. The method is applicable to various types of high-speed countercurrent chromatographs and preparation of isoflavones with different content, and has the characteristics of large separation quantity, high recovery rate and simpleness and convenience of operation.