Baicalin, baicalein, and wogonin were accumulated in hairy roots derived from Scutellaria lateriflora and Scutellaria baicalensis. The levels of baicalein and baicalin were 6.8 and 5.0 times higher, respectively, in S. baicalensis than in S. lateriflora. A total of 47 metabolites were detected and identified in Scutellaria species by GC-TOF MS. The metabolites from the two species were subjected to principal component analysis (PCA) to evaluate differences. PCA fully distinguished between the two species. The results showed that individual phenolic acids and phenylalanine, precursors for the phenylpropanoid biosynthetic pathway, were higher in S. baicalensis than in S. lateriflora. This GC-TOF MS-based metabolic profiling approach was a viable alternative method to differentiate metabolic profiles between species.