In traditional Chinese medicine practice, white ginseng (WG) and red ginseng (RG) have traditionally been used for different purposes. In the present study, an ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS)-based metabolomics approach was developed to evaluate the holistic qualities and to explore characteristic chemical components of commercial WG and RG. Through unsupervised principal component analysis (PCA) and supervised orthogonal partial least squared discrimination analysis (OPLS-DA) of the data from UPLC-QTOF-MS/MS, holistic quality inconsistencies of commercial WG and RG were identified, and the possible reasons involved were deduced by further elucidating the characteristic components of the groups. Heat treating and sulfur-fumigation were likely the main reasons for the quality differences in WG, and non-standardized processing procedures might have caused the inconsistent quality of RG. Together with ginsenoside Rg(3), a nitrogen-containing component and ginsenoside 20(R)-Rh(1) were detected as characteristic components of RG, whereas malonyl ginsenoside Rb(1)/isomer and malonyl ginsenoside Rg(1)/isomer were found to be characteristic components of WG. It was suggested that post-harvest handling procedures for WG and processing procedures for RG should be standardized using the identified characteristic components as chemical markers to ensure the consistent quality and consequently the efficacy of WG and RG.