Jian'er Xiaoshi oral liquid (JEXS), a traditional Chinese medicine (TCM) prescription, has been principally applied to treat spleen deficiency with gastrointestinal dysfunction in children caused by improper diet. However, due to a lack of research on the holistic component and metabolism of JEXS, the bioactive components of it remain unclear, hindering further study on its quality control and in vivo activity mechanism. In present study, an integrated analysis strategy based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF-MS/MS) was established to systematically screen the components and the in vivo xenobiotics of JEXS. Totally 142 compounds in JEXS were characterized, 54 of which were identified. Besides, 178 xenobiotics were detected, including 52 prototypes and 126 metabolites, while the in vivo metabolic modes of chrysin-C-glycosyls and sinapinic acid derivatives were elucidated for the first time. Our investigation gave a comprehensive analysis of the compounds and metabolic characteristics of JEXS which indicated the direction of finding the bioactive ingredients and will provide an important basis for quality control and further study on the pharmacodynamic mechanism of JEXS.