Panax notoginseng (Burk.) F.H. Chen, also known as Sanqi, is a high‐value Chinese medicine with a hemostatic effect. It was mainly used to treat traumatic and ischemic cardiovascular diseases. According to different harvest times, Panax notoginseng is divided into “Chunqi” and “Dongqi.” To effectively classify them, a high‐performance liquid chromatography coupled with a chemical pattern recognition method was established. Similarity analysis, principal component analysis, and orthogonal partial least squares discriminant analysis were applied to classify and evaluate 35 batches of Panax notoginseng. The results showed that similarity analysis based on the peak area of 20 components could not achieve accurate classification. Principal component analysis and orthogonal partial least squares discriminant analysis methods could clearly classify Chunqi and Dongqi. In order to find definite chemical markers and simplify the established model of orthogonal partial least squares discriminant analysis, seven characteristic peaks with higher variable importance in projection values were selected. As a result, this method could be used for the classification of Chunqi and Dongqi, which showed an excellent potential application for quality evaluation of Panax notoginseng.