In this study, we aim to determine the chemical constituents of six Chinese medicinal materials from the Citrus genus using high‐performance liquid chromatography and high‐resolution mass spectrometry. Eight flavonoids and one coumarin were identified and further quantified as marker substances by high‐performance liquid chromatography method. The separation was performed on an Agilent TC‐C18 column with 0.1% formic acid and acetonitrile as the mobile phase under gradient elution. The analytical method was fully validated in terms of linearity, sensitivity, intra‐ and inter‐day precision and repeatability, limit of detection, limit of quantitation, and recovery. It was subsequently applied to evaluate the quality of 103 batches of the Chinese medicinal materials from the Citrus genus. In addition, the principal constituent analysis was used to compare the samples of different species from the Citrus genus leading to successful classification of the samples in accordance with their origins. It was found that the contents of nine constituents varied greatly in different ripening stages and varieties of the samples from the Citrus genus. In addition, neoeriocitrin and 5,7‐dimethoxycoumarin were determined as two unique constituents of ‘Zhiqiao’ and ‘Foshou’, respectively. In conclusion, this study provides a chemical basis for quality control of Chinese medicinal materials from the Citrus genus.