Muscle deterioration caused by endogenous enzymes can greatly impact the quality of shrimp products during their processing and storage. In this study, the changes in trypsin, calpain, and cathepsin activity and their effects on muscle proteins in the intact and beheaded shrimp during 120 days of frozen storage were investigated. The results showed that the hardness, stretching force, chewiness, myofibrillar protein (MP) content, and Ca2+-ATPase activity significantly decreased in both the intact and beheaded shrimp samples with the prolonged storage period. Notably, the beheaded shrimp exhibited more stable characteristics than the intact shrimp samples throughout frozen storage. The endogenous enzyme analysis showed that the variations in the trypsin, calpain, and cathepsin activities were significantly pronounced in the intact shrimp compared to those in the beheaded samples. Furthermore, the myofibrillar fragmentation index, SDS-PAGE, and histological structure analysis revealed that the beheading treatment on the shrimp greatly inhibited the dissociation of muscle proteins during frozen storage. Our findings showed that the trypsin in the head of shrimp could be transferred to muscle tissues through the first abdominal segment during long-term storage, thus accelerating the degradation of MPs in the muscle tissues. Therefore, the beheading treatments effectively prolonged the shelf-life of stored shrimp products. •Alterations in endogenous enzymes in intact and beheaded shrimp were investigated.•Physicochemical properties of muscle proteins decreased with prolonged storage period.•Endogenous enzymes induced damage on MPs during storage.•Beheaded shrimp exhibited stable characteristics than intact samples.•Trypsin might be transferred from head to muscle accelerating degradation of MPs.