The quality of medicinal herbs and their products is steadily becoming important in tandem with growing interest in complementary alternative medicine for treatment of diseases. Chemical assays with bioactive secondary compounds are usually used for chemical standardization in herbs for quality control purpose. In this study, an analytical platform comprising of a GC/MS technique with an unsupervised multivariate analysis and a complementary one-dimensional 1 H NMR technique was used to obtain the primary metabolite profiling of Scutellaria baicalensis obtained from different medical halls in Singapore. The key primary metabolites such as sucrose, proline, phenylalanine, fructose, and butanedioic acid for the biosynthesis of bioactive secondary metabolites in this medicinal herb were successfully characterized by the combination of the chromatography and spectroscopy techniques. Their results suggested that these compounds could serve as markers for quality control of the herb. The principal component analyses of the GC/MS data reliably discriminated between the various Scutellaria samples indicating that the developed platform was comprehensive and was applicable to assess the quality of other medicinal herbs.