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Abstract Background Chaenomelis Fructus is a type of traditional medicine used in China. At present, the quality standard of Chaenomelis Fructus is mainly based on the content of each component as a control index, lacking overall control. To improve the rapid identification of chemical ingredients for Chaenomelis Fructus, a new approach to the construction for Chaenomelis Fructus is presented in this paper. Methods The precision, repeatability and stability of the proposed HPLC method were validated in the study. Twenty batches of Chaenomelis Fructus samples from their geographical origin were analyzed by the HPLC method. Common peaks in the chromatograms were adopted to calculate their relative retention time and relative peak area. The chromatographic data were processed by the Similarity Evaluation System for Chromatographic Fingerprint of Traditional Chinese Medicine software (Version 2004 A) for similarity analysis. Results The HPLC method demonstrated satisfactory precision, repeatability and stability. The similarities of the 20 Chaenomelis Fructus samples were 0.967, 0.979, 0.965, 0.992, 0.994, 0.988, 0.974, 0.909, 0.993, 0.894, 0.983, 0.976, 0.992, 0.960, 0.990, 0.992, 0.901, 0.815, 0.947, and 0.504, indicating that the similarities of 19 samples showed a similar pattern with the exception of sample 20. Sample S20 could be considered adulterated. This was further confirmed by principal component analysis and hierarchical clustering analysis. The HPLC fingerprints of different Chaenomelis Fructus had obvious differences in area of common peaks, but less differences in the number of common peaks. Conclusions The chromatographic fingerprint of Chaenomelis Fructus with high characteristics and specificity can be used as a reference to control its quality, providing a fast quality evaluation tool for distinguishing between the authentic Chaenomelis Fructus and the adulterated products.