Metabolites are essential intermediate products in metabolism, and metabolism dysregulation indicates different types of diseases. Previous studies have shown that cigarette smoke dysregulated metabolites; however, limited information is available with electronic cigarette (E-cig) vaping. We hypothesized that E-cig vaping and cigarette smoking altered systemic metabolites, and we propose to understand the specific metabolic signature between E-cig users and cigarette smokers. Plasma from non-smoker controls, cigarette smokers, and e-cig users were collected, and metabolites were identified by UPLC–MS (Ultraperformance liquid chromatography-mass spectrometer). Nicotine degradation was activated by e-cig vaping and cigarette smoking with increased concentrations of cotinine, cotinine N-oxide, (S)-nicotine, and (R)-6-hydroxynicotine. Additionly, we found significant decreased concentrations in metabolites associated with tricarboxylic acid (TCA) cycle pathways in e-cig users verses cigarette smokers, such as: D-glucose, (2R,3S)-2,3-dimethylmalate, (R)-2-hydroxyglutarate, O-phosphoethanolamine, malathion, D-threo-isocitrate, malic acid, and 4-acetamidobutanoic acid. Cigarette smoking significant up-regulated sphingolipid metabolites, such as D-sphingosine, ceramide, N-(octadecanoyl)-sphing-4-enine, N-(9Z-octadecenoyl)-sphing-4-enine, and N-[(13Z)-docosenoyl]sphingosine, verses e-cig vaping. Overall, e-cig vaping dysregulated TCA cycle realted metabolites while cigarette smoking altered sphingolipid metabolites. Both e-cig and cigarette smoke increased nicotinic metabolites. Therefore, specific metabolic signature altered by e-cig vaping and cigarette smoking could serve as potential systemic biomarkers for early cardiopulmonary diseases.