Jinlianhua Decoction (JD), composed of Flos Trollii, Herba Taraxaci, Folium Isatidis, Radix Puerariae Lobatae, and Folium Perillae in a ratio of 6:15:10:10:6, is a prescription for Fengwen which is a group of febrile diseases due to wind in Chinese medicine. It was originally used for the prevention and treatment of severe acute respiratory syndrome (SARS), and could also be used to treat influenza due to their common pathomechanism. To elucidate the unclear pharmacodynamic basis of JD, the LC-QExactive-MS system was used to qualitatively analyze its main components in this study. As a result, 89 compounds were identified and 24 important ones were selected thereby to further perform the simultaneous quantification in 8 batches of JD samples using LC-QTrap-MS with multiple reaction monitoring (MRM). Based on the qualitative and quantitative results in combination with the bioactivities reported, 16 compounds including orientin, 2″-O-β-l-galactopyranosylorientin, puerarin, trollisin I, rosmarinic acid, 2″-O-(2'″-methylbutanoyl) isoswertisin, daidzin, scutellarin, 3'-methoxy puerarin, vitexin, 3'-hydroxy puerarin, 2″-O-(2'″-methylbutanoyl) vitexin, kaempferol, caffeic acid, 3,4-dimethoxybenzoic acid, and cynaroside were determined as the major components of JD. This study provides a useful combinational method for analyzing the major pharmacodynamic substances of JD and lays a foundation for the quality control research of the decoction.