BackgroundCitri Exocarpium Rubrum (CER), which is known as Juhong in Chinese, is the dried exocarp of Citrus reticulata Blanco and its cultivars (Fam. Rutaceae) and is currently used in Chinese medicine to protect the stomach and eliminate dampness and phlegm. The main aim of this study was to develop a high-performance liquid chromatography ultraviolet mass spectrometry (HPLC-UV-MS) method for determining the chemical compositions and fingerprint of CER. We also evaluated the antioxidant properties of CER based on its 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity, ferric ion reducing antioxidant power (FRAP) and trolox equivalent antioxidant capacity (TEAC) assays.MethodsTen CER samples were collected from Hong Kong and mainland China. Each CER sample was extracted using an ultrasonic extraction method. Chromatographic separation was achieved using a conventional Dikma Inspire C18 column with photo diode array detection (190–400 nm). Hesperidin, nobiletin and tangeretin were quantified based on the UV signal observed at 330 nm. The column was eluted with a mobile phase consisting of water and acetonitrile (15–55%) over 55 min. Fingerprints combined with similarity and principal component analyses were used to classify the herbs. The DPPH free radical scavenging activity, FRAP and ABTS properties of the different CER samples were assayed. Bivariate correlation analysis was performed to investigate the correlation between the characteristic peaks and their antioxidant capacities.ResultsLimit of detection (LOD), limit of quantification (LOQ), linearity, inter-day precision, intra-day precision, repeatability, stability and recovery of the developed method were validated, and the method was subsequently used to determine the contents of hesperidin, nobiletin and tangeretin, and to acquire the fingerprints of the CER samples. Seventeen characteristic peaks were found in the fingerprints, and eleven of them were identified. Bivariate correlation analysis revealed correlations between the characteristic peaks and the antioxidant activities of the samples.ConclusionAn HPLC-UV-MS method was developed and validated after a detailed investigation on extraction of chemical compounds from CER using different solvents and extraction times. None of the peaks was correlated with the DPPH free radical scavenging activity or ferric reducing capacity. Most of the peaks were correlated well with the ABTS radical scavenging capacity.Electronic supplementary materialThe online version of this article (doi:10.1186/s13020-017-0127-z) contains supplementary material, which is available to authorized users.