2,3,5,4'-Tetrahydroxystilbene-2-O-β-d-glucoside (THSG), a polyphenol stilbene compound, is the main active constituent in Polygonum multiflorum. In this study, a comprehensive analytical strategy was developed for the characterization of THSG metabolites in vivo (rat plasma, bile, urine, heart, liver, spleen, lung, kidney, and stomach) utilizing ultrahigh performance liquid chromatography coupled with Q Exactive hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-Q Exactive-Orbitrap MS) based on multiple data-processing techniques. As a result, a total of 75 metabolites were characterized in bio-samples, and calculated Clog P values were further employed to assign the chemical structures of some isomers. Glucoside hydrolysis, hydrogenation, hydroxylation, glucuronide conjugation, and sulfate conjugation would be the major metabolic pathways of THSG. It appeared that most metabolites would generally undergo phase I reactions followed by phase II reactions. These results provided valuable information for in-depth understanding of the safety and efficacy of THSG and showed a valuable methodology for metabolic characterization.