The addition of microbial transglutaminase (MTGase) in surimi gel protein promote cross-linking and improvement of textural properties. In this study, the effects of cross-linking by MTGase on digestibility by pepsin were investigated using different methods, including, scanning electron microscopy (SEM), particle size, dry matter digestibility, Tricine SDS-PAGE, LC-MS/MS, and analysis of amino acids. Gel properties and cross-linking of surimi gels increased significantly (P < 0.05) when surimi was induced by MTGase. Gels with MTGase prohibited the hydrolysis at the beginning because enhanced cross-linking reduced the accessibility of pepsin to the hydrolytic site and the hydrolysis rate increased more rapidly once the network was destroyed during the first 30 min of digestion. The amounts of peptides and amino acids reached their maximum at the end of digestion and showed slight difference to the control gels. The digestion sites and the quantities of peptides from myosin heavy chain also differed between two kinds of surimi gels. This research can help explore the impact of structure on surimi foods, which will improve elastic texture, nutritional value, and provide a delayed reaction in digestion that potentially enhances the feeling of satiety; this delay could control caloric intake without affecting food value.