In this study, the effects of low-temperature long-time (LTLT) processing on the quality of Patinopecten yessoensis adductor muscle (PYAM) were investigated at 55°C. The texture of processed PYAM was characterized by textural profile analysis (TPA), and significant increases of cook loss, hardness, and shear force with time during LTLT processing were observed. The degradation of structural proteins was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and fragments with molecular weights of 208 kDa (myosin heavy chain, MHC), 97 kDa (paramyosin) and 35–40 kDa, respectively, were among the main products. Chemical characterization revealed elevated levels of activity in cathepsin L and caspase-3 and oxidation of proteins and lipids. Electron spin resonance spin trapping indicated reactive oxygen species (ROS) production in the PYAM during LTLT processing. Based on these results, it is proposed that the sequence of events in PYAM during LTLT processing includes ROS→ endogenous enzyme (involving caspase-3 and cathepsin L) activation →protein degradation→quality changes (texture and color). This revelation helps to further our understanding of the LTLT processing of PYAM, which would lead to better quality control for PYAM products.