In this study, we found that dielectric barrier discharge cold plasma (CP) treatment was effective in preserving fruit quality and inhibiting the growth of microorganisms in blueberries, especially in maintaining the firmness, sugars, and ascorbic acids. In addition, the levels of total phenols, flavonoids, and anthocyanins were also elevated by CP treatment in blueberries, indicating that CP affected the phenolic metabolism. Furthermore, metabonomic study identified 59 substances, which can be divided into 9 categories. Blueberries treated with CP exhibited higher fold change values of chalcones, dihydroflavonols, dihydroflavones, flavanols, flavones, procyanidins, and anthocyanins but exhibited lower fold change values of L-phenylalanine than those in control. The activities of five key enzymes of phenylpropanoid metabolism, especially those of phenylalanine ammonia lyase, chalcone synthase, and UDP-glucose:flavonoid 3-O-glucosyltransferase, in blueberries treated with CP were higher than those in controls. These results together indicated that CP treatment affected the conversion of L-phenylalanine to phenols, flavonoids, and anthocyanins through the regulation of five key enzymes involved in the phenolic metabolism.