[Objectives] To explore the effects of temperature on the primary and secondary metabolism of Scutellaria baicalensis Georgi during the seed germination. [Methods] The superoxide dismutase(SOD) activity was determined using riboflavin-NBT; peroxidase(POD) activity was determined using guaiacol colorimetric method, catalase(CAT), ascorbate peroxidase(APX), phenylalanine ammonia lyase(PAL) and cinnamic acid-4-hydroxylase(C4H) activity were detected by ultraviolet spectrophotometry, and chalcone synthase(CHS) activity and the content of secondary metabolites were measured by high performance liquid chromatography(HPLC). [Results] The germination rate, germination potential and germination index of S. baicalensis seeds were significantly affected by temperature. The most suitable temperature for the germination of S. baicalensis seeds was 25 ℃. The activities of SOD, POD and CAT in S. baicalensis seeds treated at low and high temperature were higher than that treated at suitable temperature; the activities of PAL, C4H and CHS of S. baicalensis seeds treated at low and high temperature were lower than that treated at suitable temperature. There was a good positive correlation between flavonoids and soluble sugar, PAL activity and C4H activity, and the correlation coefficients were R=0.894*, R=0.956* and R=0.951*, respectively. [Conclusions] In adverse environment, S. baicalensis seeds have good defense capabilities. During the germination of seeds, the formation of secondary metabolites is significantly correlated to the activity of key enzymes. Therefore, high-quality medicinal materials can be obtained by taking measures to improve the activity of key enzymes.