This study analyzed the effects of ecological factors on secondary metabolites of Scutellaria baicalensis using two sources: 92 individual roots of S. baicalensis from all over China, and secondary metabolites, medicinal materials and inorganic element contents obtained from the testing of 92 S. baicalensis rhizosphere soil samples. The study used environmental data from the Genuine Medicinal Material Spatial Analysis Database. Most of the chemical constituents of S. baicalensis were negatively correlated to latitude and positively correlated to temperature; generally, the contents of 21 chemical constituents were higher at low latitudes than that at high latitudes. By gradual regression analysis, it was found that the content of baicalin in S. baicalensis was negatively correlated to latitude and generally the content of inorganic elements in soil was excessively high (excluding Mg and Ca), which has a negative effect on the accumulation of chemical constituents in S. baicalensis. Based on the cluster analysis of 21 constituents, S. baicalensis from different places of origin was divided into two groups, and S. baicalensis was not genuine only in a specific small region. Within the zone from Chifeng, Inner Mongolia to Taibai, Shaanxi is suitable for accumulation of secondary metabolites of S. baicalensis and such a zone represents a suitable distribution and potential genuine producing area.