Scutellaria Radix, a traditional Chinese medicine, studies on its main active ingredient are limited. In this study, the purpose was to investigate the quality difference of Scutellariae Radix from different origins based on chemical components and biological activities. The chromatographic fingerprints of Scutellariae Radix from 33 origins were established using HPLC, and the antibacterial activities were studied with the microdilution method. Moreover, orthogonal partial least-square regression, pearson correlational analysis and grey relational analysis methods were performed to explore the relationship between the compositions and bioactivities. In addition, and origin identification model was established to comprehensively evaluate the quality of Scutellariae Radix. The results showed that Scutellariae Radix had in-vitro antibacterial effect on Staphylococcus aureus, and the best were in Gansu, Shandong Province. Multivariate statistical analysis common showed that three components were positively correlated with antibacterial activity, which were respectively wogonin, baicalein and oroxylin. In conclusion, the quality of Scutellariae Radix varies greatly from different origins, and the better was in Gansu and Shandong Province. This work successfully provides a general model that combined the chromatographic fingerprint and bioactivity assay to study the spectrum–effect relationships, which could be used to discover the primary active ingredients in traditional Chinese medicines.