Browning is a critical problem, which often limits the shelf life and marketability in fresh-cut lotus tuber. Proteome level changes in response to the browning metabolism were investigated using two-dimensional electrophoresis (2-DE) and MALDI-TOF-TOF. A total of 34 functional protein spots were identified by comparing 2-DE protein patterns of fresh-cut lotus tuber before and after browning. These 34 identified proteins could be classified into 7 functional groups based on the NCBI database, that is, material and energy metabolism (35%), stress response (20%), respiration metabolism (12%), cell structure (12%), signal transduction (6%), gene expression regulation (6%), and unclassified proteins (9%). The group with the greatest difference in protein expression was related to material metabolism and regulation, reactive oxygen species metabolism, and respiratory control. The distinct proteins included universal stress protein (USP), superoxide dismutase (SOD), peroxidase (POD), ferritin, and ATPase.