An ultra-high performance liquid chromatography coupled with quadrupole Orbitrap mass spectrometry (UHPLC-Q-Orbitrap/MS)-based metabolomics method was applied to investigate the chemome diversity of Schisandra chinensis fructus (SF) and its processed products, including vinegar-processed Schisandra (VS), wine-processed Schisandra (WS), and honey-processed Schisandra (HS). A clear classification among four Schisandra products was observed in the score plot of the partial least-squares discriminant analysis (PLS-DA) model, then 28 marker compounds were selected and identified. The content of most marker compounds in VS and WS was increased compared with that in SF, and the lowest content was observed in HS, then the high-performance liquid chromatography (HPLC) analysis was performed to confirm the change trends. These results suggested the chemical composition variation occurs in different Schisandra products, and the marker compounds selected in this study will be useful for the quality evaluation of Schisandra products.