Wu Ji Bai Feng Pill (WJBFP) is a traditional Chinese medicine (TCM) complex formula, which has been widely used in the treatment of various gynecological disorders. However, the quality control of multiple components in WJBFP is challengeable by using the methods applicable to analysis of several phytochemicals in single herbs or simple herbal preparations. The purpose of this study is to establish an ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC–MS/MS) method for the quantitative determination of 20 bioactive compounds in WJBFP. The modified chromatographic conditions were achieved on an Agilent Poroshell 120 EC-C 18 column with a gradient elution consisted of 0.1% formic acid in acetonitrile and 0.1% aqueous formic acid (v/v). All analytes were determined using a triple quadrupole mass spectrometry in positive or negative ionization modes with multiple reaction monitoring (MRM) mode. An UHPLC–MS/MS method was optimized and validated for linearity, limits of detection and quantification, precision, repeatability, stability and recovery. The proposed method was applied for the analysis of 20 compounds in 19 batches of commercial WJBFP products. principal component analysis and hierarchical cluster analysis were applied to evaluate intrinsic quality and to identify chemical markers most responsible for quality evaluation. In conclusion, the established method offered speedy and sensitive determination for 20 compounds and is helpful for chemical standardization of commercial WJBFP products.