Abstract: In this study, a high-performance liquid chromatography method was established to simultaneously determine three flavonoids including hesperidin (HES), nobiletin (NOB) and tangeretin (TAN) in 10 batches of Citrus reticulata 'Chachi' planted and collected in Xinhui District, Jiangmen City, Guangdong Province. Moreover, we studied the metabolism and transformation of three flavonoids in liver and intestinal flora in vitro, and sequenced 16S rRNA of bacteria flora samples after incubation. The RP-HPLC system consisted of Alltima C18 column (250 mm×4.6 mm, 5 μm) and a mobile phase of water (A)-methanol (B). The column temperature was 25℃ and the detection wavelength was both 283 nm and 330 nm while the flow rate was 1.0 mL·min^-1. The results showed that the retention time of HES, NOB and TAN ranged from 12.313 min to 34.271 min. The content of HES, NOB and TAN in 10 batches of Citrus reticulata 'Chachi' was 26.81-39.80 mg·g^-1, 4.06-7.90 mg·g^-1 and 1.81-3.93 mg·g^-1, respectively. There were differences in the content of flavonoids in different batches and growing areas. The three flavonoids were metabolized in various degrees after incubation of rat and human liver S9, cytosol, microsomes or intestinal flora in vitro, especially HES. The results of 16S rRNA showed that the main flavonoids of Citrus reticulata 'Chachi' could regulate lipid metabolism by regulating intestinal flora related to energy metabolism. This study established a rapid, simple, reproducible and stable quantitative analysis method for detecting the main flavonoids in Citrus reticulata 'Chachi' which evaluated the content of flavonoids from Citrus reticulata 'Chachi' in different growing areas and different storage periods. The intestinal bacteria can metabolize and transform the flavonoids of Citrus reticulata 'Chachi' to varying degrees, which provides a valuable scientific basis for the subsequent study on the material basis of the efficacy of Citrus reticulata 'Chachi' from the perspective of metabolism. Animal experiments were approved by the Medical Ethics Committee of Guangdong Jiangmen Chinese Medicine College (No. 20190419).