The invention discloses an analysis method for distinguishing citrus chachiensis hortorum from pericarpium citri reticulatae through HPLC finger print in combination with stoichiometry. The method comprises the following steps: performing pretreatment on citrus chachiensis hortorum samples and pericarpium citri reticulatae samples respectively, and performing gradient elution through a high performance liquid chromatograph, so as to obtain citrus chachiensis hortorum common mode finger print, analyzing finger print information, so as to obtain 17 common peaks of aurantiamarin taken as a reference peak, and identifying 3 common peaks through comparison of the sample and standard substance; preprocessing HP original data of different batches of citrus chachiensis hortorum samples and pericarpium citri reticulatae samples, and then performing similarity calculation, clustering analysis and principal component analysis. The method has the advantages that analysis results are displayed in modes of similarity data range, tree clustering analysis graphics and PCA score plots, a constructed citrus chachiensis hortorum quality control mode clearly reveals the regularity and difference of citrus chachiensis hortorum from pericarpium citri reticulatae, can visually distinguish varieties of citrus chachiensis hortorum from pericarpium citri reticulatae, relevant verification and analysis are not required, quantitative difference between the varieties is embodied, and the method can serve as an analysis method for distinguishing citrus chachiensis hortorum from pericarpium citri reticulatae.