[Objective] To investigate the primary and secondary metabolism during the seed germination of Scutellaria baicalensis Georgi. [Method] The activities of SOD and POD were determined with lactoflavine-NBT method and guaiacol-colorimetry as- say, respectively. The activities of CAT, APX,PAL and C4H were determined with ultraviolet spectrophotometry. The contents of secondary metabolites were detected by High-performance Liquid Chromatography (HPLC). [Result] The results indicate that the soluble sugar content decreased during the first 5 days and then increased when the cotyledons formed. The contents of PAL, C4H and CHS continuously in- creased at different stages during the seed germination process. The secondary metabolites also showed the consistent variation trend. In addition, the contents of secondary metabolites had significant positive correlation with the key enzyme activi- ty. [Conclusion] The formation of secondary metabolites is significantly positively cor- related with the key enzyme during the seed germination process. Therefore, the key enzyme activity can be enhanced by adopting appropriate measures to improve the secondary metabolites, thereby obtaining high-quality medicinal materials.