Lingyang Qingfei pills (LQP), the renowned traditional Chinese medicine recipe, have been extensively utilized for the therapy of xerostomia, sore throat, bronchiolitis, and pneumonia in clinics. However, its phytochemicals remain equivocal, which severely limits the development of quality control and activity mechanisms. In the current research, a trusted method founded on ultra-high performance liquid chromatography with Quadrupole-Exactive Orbitrap mass spectrometry technique was proposed for the comprehensive screening of in vitro and in vivo chemical compositions of LQP. As a consequence, 239 constituents were preliminarily characterized, 37 of which were accurately confirmed by reference standards. In addition, a total of 208 xenobiotics, containing 71 absorbed prototypes and 137 metabolites, were revealed in rat plasma, bile, urine, and feces, respectively. The metabolic reaction of hydrolysis, hydroxylation, methylation, glycosylation, sulfation, and mixed-mode was detected in the biotransformations of flavonoids, terpenoids, alkaloids, anthraquinones, organic acids, phenylpropanoids, and so forth. And 12 of the metabolites were new compounds. This experiment acted as the first reference for chemical substances and metabolites of LQP, which could provide valuable chemical information for further clarifying pharmacodynamic substances and pharmacokinetic studies.