Salvia miltiorrhiza, also known as Danshen, is a widely used traditional Chinese medicine for the treatment of cardiovascular diseases and hematological abnormalities. The root and rhizome of Salvia przewalskii and Salvia yunnanensis have been found as substitutes for Salvia miltiorrhiza in the market. In this study, the chemical information of 14 major compounds in Salvia miltiorrhiza and its substitutes were determined using a high-performance liquid chromatography method. Stepwise discriminant analysis was adopted to select the characteristic variables. Partial least squares discriminant and hierarchical cluster analysis were performed to classify Salvia miltiorrhiza and its substitutes. The results showed that all of the samples were correctly classified both in partial least squares discriminant analysis and hierarchical cluster analysis based on the four compounds (caffeic acid, rosmarinic acid, salvianolic acid B, and salvianolic acid A). This method can not only distinguish Salvia miltiorrhiza and its substitutes, but also classify Salvia przewalskii and Salvia yunnanensis. The method can be applied for the quality assessment of Salvia miltiorrhiza and identification of unknown samples.