Ginsenosides in Panax ginseng are regarded to be functional ingredients for diverse pharmacological effects and orally administrated with very low absorption in the gastrointestinal tract to be metabolized by gut microbiota. However, in vivo metabolic characteristics of ginsenosides mediated by gut microbiota are not well-known. This study aimed to explore the metabolic profiles of ginsenosides in rat feces mediated by gut microbiota. Ginsenosides and metabolites were identified and relatively quantified by ultra-performance liquid chromatography tandem/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS). As a result, eighty-four metabolites were identified in the normal control rat feces, while only thirty intermediates were found with very low yields in the pseudo-germ-free (GF) group. Similarly, the main bioconversion pathways of ginsenosides in vivo were the same deglycosylation reaction mediated by gut microbiota in vitro. The findings demonstrated significant differences in metabolic profiles between the normal control and pseudo-GF rats, which implied gut microbiota played an important role in the metabolism of ginsenosides.