To clarify the metabolic transformation mechanism of phenylethanoid glycosides in Xiaoer Chiqiao Qingre Granules in vivo, this study extracted and separated the phenylethanoid glycosides in Xiaoer Chiqiao Qingre Granules. Based on UPLC-Q-TOF-MS/MS technology, the retention time and primary and secondary mass spectrometry information were analyzed by UNIFI software, and 11 phenylethanoid glycosides in Xiaoer Chiqiao Qingre Granules were preliminarily identified. Sixty-nine metabolites related to phenylethanoid glycosides were identified from the plasma samples of juvenile rats after administration of Xiaoer Chiqiao Qingre Granules. In addition, this study simulated the transformation system of intestinal flora in children, and discussed the metabolic effects of intestinal flora on the representative components forsythoside A, forsythoside E, and salidroside of phenylethanoid glycosides. The model of gastrointestinal heat retention in children with food accumulation was established to study the differential metabolites of phenylethanoid glycosides. Through the comparative analysis of the representative components absorbed in blood and the intestinal floral transformation products, it was found that the main metabolic pathways of phenylethanoid glycosides were dehydrogenation, oxidation, acetylation, sulfation, and glucuronidation. The findings of this study revealed the transformation law of phenylethanoid glycosides in the gastrointestinal tract. Through the preliminary discussion of the pharmacological mechanism, this study provides references for further clarifying the pharmacodynamic material basis of Xiaoer Chiqiao Qingre Granules and exploring the pediatric Chinese medicine compound.