Cold atmospheric plasma (CAP) is a novel technology which is widely used in the biomedical field and has developed quickly over the past few years, especially in cancer therapy. Compared to traditional anti-cancer approaches, CAP treatment shows a selective anti-cancer mode which makes CAP a promising anti-cancer treatment modality. However, the underlying mechanism of this selective cytotoxicity is not fully elaborated. In this study, we demonstrated that A375 human melanoma cells were more sensitive to CAP treatment than HaCaT cells and compared the differences in metabolites of these two cell lines after CAP treatment. Using ultra-high performance liquid tandem chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) approach, we identified 361 changes (metabolites) in HaCaT cells and 1531 changes in A375 cells. Further research using KEGG pathway analysis found that purine metabolism and Pantothenate and CoA biosynthesis were highly correlated with changes of HaCaT cells and A375 cells after CAP treatment. Our results shed light on the mechanism of selective cytotoxicity in the metabolites' aspect.