Angong Niuhuang Pill (ANP) is a traditional Chinese medicine (TCM) formula with significant clinical efficacy in the treatment of stroke. Due to its complex composition, little attention has been directed toward the analysis of chemical composition and absorption characteristics of ANP. In this study, a reliable two-dimensional ultra-highperformance liquid chromatography (2D-UHPLC) coupled with quadrupole-Orbitrap high-resolution mass spectrometry (Q-Orbitrap HRMS) method was established to characterize the chemical constituents in ANP as well as the prototype components and metabolites absorbed in plasma, urine, feces, and brain tissues after oral administration. The prototype components were identified by a high mass accuracy (within 5 ppm) and MS/MS data based on online, local, and ANP self-built databases. The metabolites were predicted and identified using Compound Discoverer metabolic platform. A total of 154 compounds mainly including 37 flavonoids, 35 alkaioids, 19 organic acid, 19 bile acid, 32 terpenoids and 12 others were identified in this way. In addition, 60 prototype components mainly including flavonoids, alkaioids, organic acid, terpenoids and 164 metabolites were confirmed or preliminarily identified in rats. The metabolic pathways phase I reaction (hydration, reduction, oxidation, demethylation, and hydroxylation) and phase II reaction (acetylation, stearyl conjugation, and methylation) for the absorbed constituents were explored and summarized. This is the first systematic and comprehensive chemical characterization in ANP and its metabolism in vivo by 2D-UHPLC-Q-Orbitrap HRMS. This approach provides an effective strategy for the characterization of compounds and metabolites in traditional Chinese medicine formulas.