Enzymatic browning of fresh-cut potatoes (Solanum tuberosum L.) is an urgent problem to be solved in the potato industry. The transcript level of snakin-2 (StSN2) increased with prolonged fresh-cut potato storage time, and StSN2 overexpression reduced the enzymatic browning of fresh-cut potato compared to wild type (WT). Further studies suggested that overexpression of StSN2 effectively enhanced polyphenol oxidase (PPO), peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) activity, decreased phenolic and soluble quinone contents. The measurement of total free amino acid results showed that the contents of proline, isoleucine, and gamma-aminobutyric acid were increased, and the contents of cystine, methionine, and tyrosine were decreased in StSN2-overexpressing transgenic lines. Quantitative phosphoproteome analysis showed that 1515 proteins were phosphorylated in transgenic fresh-cut potato. Among them, 123 kinases were found to change phosphorylation levels, and a kinase-substrate network of serine/arginine proteins and mitogen-activated protein kinases was predicted. Our results indicated that overexpression of StSN2 inhibited the enzymatic browning of fresh-cut potatoes by enhancing antioxidant enzyme activity and decreasing phenolic and soluble quinone contents while also changing vital kinase and other protein phosphorylation levels. This study demonstrated a new function of StSN2 and provided target genes for enzymatic browning resistance breeding of potatoes.