A high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry method was developed and validated for the determination of flavonoid glycosides, polymethoxyflavones, and coumarins in herbal medicines of Citrus fruits and peels and Poncirus fruits. The analytes were rutin, narirutin, naringin, hesperidin, neohesperidin, neoponcirin, poncirin, naringenin, sinensetin, isosinensetin, nobiletin, heptamethoxyflavone, tangeretin, imperatorin, phellopterin, and isoimperatorin, and, together with puerarin (the internal standard), were separated in short run time using a gradient flow of acetonitrile and 0.1% formic acid. Mass spectrometry detection was performed in the multiple reaction monitoring mode. Ion detection was operated alternately between negative and positive ion modes in a single injection. The main fragmentation characteristics of the analytes were investigated to discriminate between isomeric pairs. Validation of the analytical method showed linearity, r > 0.999; accuracy, 96.2 to 103.4%; and precision, relative standard deviation <4.2%. The method was employed to determine these compounds in the following herbal drugs: Citri Unshius Pericarpium, Citri Unshius Pericarpium Immaturus, Ponciri Fructus Immaturus, Aurantii Fructus Immaturus, and Aurantii Fructus. The analytical results showed that there were significant differences between different varieties, different herbal origins, and production areas. This study demonstrated that this method may be used to monitor quality control of the herbal drugs and perform chemotaxonomic investigations.