The aim was to establish a method for the determination of twelve flavonoid components in Scutellaria baicalensis. The HPLC method was performed on an Agilent ZORBAX SB-C18 column (4.6 mm×150 mm, 5μm) with a detection wavelength of 280 nm and a mobile phase of acetonitrile-0.1% phosphoric acid aqueous solution at a flow rate of 1.0 mL/min and a sample volume of 10 μL. The established extraction and chromatographic conditions were used for the qualitative and quantitative analysis of Scutellaria baicalensis. The linearity of the twelve flavonoids in Scutellaria baicalensis was good in the mass concentration range (r>0.98), and the average spiked recoveries of scutellarin, apigenin-7-O-β-D-glucopyranoside, carthamidin, baicalin, luteolin, chrysin-7-O-glucuronide, wogonoside, apigenin, baicalein, wogonin，chrysin and oroxylin A were 99.7214%, 92.7039%, 103.9755%, 100.5837%, 92.4819%, 93.2465%, 99.6387%, 104.3866%, 95.0767%, 95.3245%, 92.2161%, 95.3995% (RSD<5). A method for the determination of twelve flavonoid components in Scutellaria baicalensis was established, which was easy to operate, reproducible and accurate.