A liquid chromatography-electrospray ionization-mass spectrometry method has been developed and validated for identification and quantification of four major bioactive saponins in rat plasma after oral administration of extraction of saponins from Flos Lonicerae, i.e., Macranthoidin B, Macranthoidin A, Dipsacoside B, and Macranthoside B. The retention time of Macranthoidin B, Macranthoidin A, Dipsacoside B, Macranthoside B and IS are 10.65, 12.11, 13.81, 23.31 and 5.47 min, respectively. Taking Macranthoidins A, B, Dipsacoside B (saponins), sweroside (iridoids), and luteolin-7-O-d-glucoside (flavonoids) as markers, a method of ultra high performance liquid chromatography with triple quadrupole mass spectrometry is employed to determine their amounts in Lonicerae Flos, Lonicerae Japonicae Flos, and Lonicerae Japonicae Flos preparations.