Scutellariae Radix (SR), the dried root of Scutellaria baicalensis Georgia, is a famous Chinese materia medica that has been widely employed. Raw Scutellariae Radix (RSR), steamed Scutellariae Radix (SSR), and wine Scutellariae Radix (WSR) are adopted for use in clinical practice. Because of their easily confused appearance, they are always misused. Aiming at this problem, an ultra performance liquid chromatography coupled with photodiode array detector (UPLC-PDA) method was established to survey misuse of the RSR and the processed SR (SSR and WSR) in the market by employing baicalin (BC), wogonoside (WS), baicalein (BN), and wogonin (WN) as quality indicators. Fortunately, β-glucuronidase, which mediates conversion from flavone glycoside to aglycone, was identified in the RSR samples by the sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The significant production of BN and WN was witnessed in the RSR samples, which did not occur in the SSR and WSR samples in virtue of the inactivated β-glucuronidase. Besides, the different capacities of β-glucuronidase were evaluated in the tested samples. In general, we provided the first evidence to scientifically identify RSR from SSR and WSR.