An approach was established to analyze the chemical profiling of Xiao-Cheng-Qi Decoction (XCQD) using liquid chromatography coupled with electrospray ionization tandem mass spectrometry. XCQD consisted of three herbal medicines (Rhubarb, Fructus Aurantii Immaturus and Cortex Magnoliae Officinalis). The traditional water extractive method was applied in the sample preparation, which was identical with clinical use. The characteristic fragmentation pathways of 17 reference compounds were comprehensively studied, including precursors of tannins, flavonones, anthraquinones and lignan. In total, 71 constituents were identified or tentatively characterized based on their mass spectrometry fragmentations and chromatographic behaviors. By comparing their relative contents, flavanones and anthraquinones were supposed to be used together for the quality control of XCQD. Further pharmacology and pharmacokinetics investigations should be performed on the basis of the present chemical profiling study.