Abstract: Flavan-3-ols are important dietary polyphenol, their bioavailability are not only limited to the parent compound, but also the metabolites after the intestinal microbial metabolism in vivo. Aimed to identify the in vivo metabolism and the contribution of metabolites to bioavailability, the quantitative analysis methods of dietary flavan-3-ols and their metabolites were researched. According to the difference response values of the product ions of each compound, the appropriate concentration in the mixed standard was determined, and the quantitative analysis method of ultra-high performance liquid chromatography-triple quadrupole tandem mass spectrometry (UHPLC-QQQ-MS) was established. All compounds had good resolution and appropriate response values within analysis time of 15 min. The method validation results showed that most of the quantitative compounds had good linearity. Urine, feces and plasma were used as samples to investigate the intra-day and inter-day precision of the method. The RSD value of the method was below 15%, the matrix effect was within ±20%, and the recovery was mainly between 70% and 120%. The method is fast, sensitive, accurate and stable, which can be used as a method for targeted quantitative research of flavan-3-ol compounds in vivo.