Malondialdehyde (MDA), a reactive lipid-oxidation product formed during meat processing, can modify myosin and reduce its gastric digestibility. However, MDA's effects on myosin digestibility during heating and their structural basis remain unclear. Purified porcine myosin was treated with 10–50 mmol/L MDA and heated at 100–180 °C for 10–30 min. Pepsin hydrolysis, secondary structure, fluorescent MDA-related products, ζ-potential and particle-size distribution were analysed. MDA significantly reduced susceptibility to pepsin hydrolysis; its concentration was more negatively associated with gastric digestibility ( r = −0.60 ) than heating temperature ( r = −0.28 ) or time ( r = −0.06 ). During heating, MDA promoted a redistribution from β-turn-dominated to β-sheet-enriched structures, increased apparent surface-charge magnitude and broadened particle-size distributions, indicating enhanced conformational rearrangement and aggregation. At 10 and 25 mmol/L MDA, fluorescence intensity was generally higher at 140 °C than at 100 °C; however, this enhancement weakened after prolonged heating and at 50 mmol/L MDA. This pattern may reflect aggregation-induced self-quenching and burial of fluorophores within compact structures. Correlation and model-assisted analyses linked α-helix/random-coil retention with higher hydrolysis, whereas β-sheet enrichment and aggregation were associated with reduced digestibility. Overall, MDA impaired the gastric digestibility of myosin during thermal processing, accompanied by secondary-structure rearrangement, altered MDA-related fluorescence, and protein aggregation.