With increasing drug resistance of Pseudomonas aeruginosa, a new sterilization method is needed. Plasma has been shown to be an effective method of sterilization, but no researchers have studied the effect of plasma on bacterial metabolism. In this paper, we studied the emission spectrum, liquid phase active particles, and other physical and chemical properties of a portable plasma device. Pseudomonas aeruginosa were then treated with activated water generated by surface plasma discharge. Using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we obtained the differential metabolite pathways. The results showed that, after plasma activated water treatment, the carbohydrate metabolism of the bacteria was inhibited and the metabolic processes of protein and amino acid decomposition were enhanced. Therefore, water activated by atmospheric-pressure cold plasma can significantly change bacterial metabolites, thus promoting bacterial death.