Precipitation was formed during the preparation of decoction from a mixture of Scutellariae Radix and Coptidis Rhizoma. Baicalin and berberine were identified in this coprecipitated product (CPP) and these components were the active ingredients of two herbal medicine. We extracted respectively crude baicalin and berberine in Scutellariae Radix and Coptidis Rhizoma and prepared coprecipitate of crude baicalin-berberine. To increase the stability and bioavailability of coprecipitate of crude baicalin-berberine(CBB), which is slightly soluble drug, its inclusion complex was prepared and studied in this experiment. Inclusion complex of CBB with ${eta}-cyclodextrin(CBB-{eta}-CD)$ was prepared by freeze drying method and its characteristics were ascertained by means of solubility test, differential thermal analysis(DTA) and scanning electron microscope(SEM). The type of $CBB-{eta}-CD$ is classified as $A_L-type$ on phase solubility diagram, and the stoichiometric ratio of CBB(baicalin in CBB) : ${eta}-CD$ complex is 1:1 and formation constant is 151 $M^-1$. The solubility, dissolution, in situ absorption and serum concentration of $CBB-{eta}-CD$ were significantly increased when compared to CBB. Therefore enhanced bioavailability of CBB by inclusion complexation with ${eta}-cyclodextrin$ might be useful for dosage form design of active ingredients of two herbal medicine.