In multicomponent drugs, such as Kampo (traditional Japanese medicine) medicines, compound–compound interactions, including synergistic effects, inhibitory effects, and complex formations, should be considered. Orengedokuto is a Kampo formula, which is used for the treatment of various diseases, including inflammation, hypertension, gastrointestinal disorders, and liver and cerebrovascular diseases. During the decoction process in the production of Orengedokuto, yellow precipitates are obtained from berberine–baicalin complexation; these precipitates enhance the in vivo coprecipitation and coabsorption of both compounds. Scutellaria root contains various baicalin analogs, such as wogonoside, oroxyloside, and scutellarin; however, the compound–compound interactions between berberine and flavonoid glycosides have not been investigated. Herein, we performed precipitation assays for berberine and the crude extract of Scutellaria root to detect and quantify compounds that interact with berberine by HPLC analysis. Furthermore, we performed precipitation assays and NMR experiments to identify chemical structures that affect the formation of precipitates; specifically, we analyzed all combinations of berberine and identified flavonoids to provide insights into associated compound–compound interactions. The NMR experiments indicated that C-8 modification affected the pi–pi interaction between berberine and flavonoids. This information enables the synthesis of more effective molecules and provides insights into their functions, such as drug delivery. The investigation of the interaction mechanisms of berberine and baicalin analogs in Kampo medicines can provide comprehensive insights regarding multicomponent drugs.