A capillary zone electrophoresis (CZE) method modified by β-cyclodextrin (β-CD) and acetonitrile (ACN) was developed for simultaneous determination of seven structurally similar flavonoids in Scutellariae Barbatae Herba (SBH) and its preparations. Molecular selectivity of the analytes by β-CD was in the following order: apigenin, luteolin, quercetin, scutellarin, baicalein, rutin and wogonin, based mainly on the "molecular fit" interaction between some ligands in the C ring of the flavonoid and the cavity of β-CD. Flavonoids with hydroxyl substituent(s) at the C-ring, especially the 4' monohydroxyl, were highly selected by β-CD although hydrophobicity of the guest molecule is the primary factor affecting the complexation. The function of acetonitrile in this study was to improve the separation of the analytes in the real SBH. The developed method was validated and applied to real samples. The principle of separation based on this CZE condition is also explained.