Commercial sterilization is a typical food processing method. The effects of commercial sterilization on nonginsenoside functional components including phenolic acids, alkaloids, flavonoids, lignins and coumarins in ginsengs were studied by widely targeted metabolomics based on UPLC-ESI-MS/MS system. These components of ginsengs were significantly distinguished using principal component analysis. The results suggested that a total of 259 non-ginsenoside functional compounds were identified, among which 46 phenolic acids, 12 alkaloids, 18 flavonoids, 12 lignins and coumarins were increased. On the contrary, 7 phenolic acids, 4 alkaloids and 5 flavonoids were decreased. This study systematically analyzed the impact of commercial sterilization on the nonginsenoside functional components in fresh ginseng pulp and provides novel reference values for ginseng processing.