Ba-Bao-Dan (BBD) is a well-known Traditional Chinese medicine (TCM) prescription in China. It was first formulated in approximately 1555 AD. As one of the National Protected TCM, it is widely used to treat jaundice, viral hepatitis, cholecystitis, acute urinary tract infection, cancer, and other diseases. It is a healthcare medicine that is used to prevent many diseases in China. In other Asian countries and in European and American countries, BBD is used as a drug to protect the liver. However, a systematic quality study on BBD chemical markers has not been carried out. This study aimed to establish an ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-MS/MS) method for the quantitative determination of 43 compounds in BBD. Furthermore, the method was used to further find chemical markers for quality control through the combination with chemometrics. The modified chromatographic conditions were achieved on Waters Cortecs C18 column (2.1 × 100 mm, 1.6 μm) with a gradient elution consisting of 0.1 % formic acid in water and acetonitrile with methanol (1:1, V/V). All analytes were determined in the multiple reaction monitoring mode. The method was validated for linearity, detection limits, precision, repeatability, stability and accuracy. The method was used to analyze the 43 compounds in 11 batches of BBD samples. Hierarchical cluster analysis and principal component analysis were applied to evaluate intrinsic quality of BBD and to identify the potential chemical markers for quality control. In conclusion, the method rapidly and sensitively determined the 43 compounds, among which 10 compounds, namely, N-Gin R1, Gin Re, Gin Rg1, Gin Rb1, GCA, Gin Rd, CA, TCA, CDCA, and DCA, were considered as the potential chemical markers for BBD quality control.