This study employed a multi-technique approach to investigate the structural and conformational changes in proteins in Meretrix lyrata (M. lyrata) adductor, foot, and siphon tissues during boiling. Data-independent acquisition (DIA) quantitative proteomics was utilized to identify differentially expressed proteins (DEPs) in six temporal comparison groups (20–0 s, 40–20 s, 60–40 s, 80–60 s, 100–80 s, and 120–100 s). The results showed that key myofibrillar proteins, including myosin heavy chain, paramyosin, and actin, exhibited tissue-specific expression patterns, while low-molecular-weight degradation fragments (<17 kDa) appeared with prolonged heating. Turbidity measurements peaked in adductor and siphon tissues at 60 s and in foot tissue at 80 s. Heating resulted in a narrowed particle size distribution (100–1000 nm), and a decreased zeta potential, indicating a reduction in protein surface charge. Fourier transform infrared spectroscopy revealed hydrogen bond disruption and secondary structure transitions, marked by a reduction in α-helix content with a corresponding increase in β-sheet and random coil structures. In total, 6527 proteins were identified, and Gene Ontology (GO) enrichment analysis highlighted the DEPs’ involvement in biological regulation and metabolic processes. Collectively, these results provide comprehensive characterization of protein denaturation, degradation, and structural reorganization in M. lyrata tissues during the boiling process.