Spice and its extracts have gained widespread utilization as natural and eco-friendly additives, imparting enhancements in flavor, color, and antioxidative attributes to meat-based products. This work aims to study the effect mechanism of capsaicin (CA) and dihydrocapsaicin (DI) in capsicum (chili pepper) on the structure and function of myofibrillar proteins (MPs) in duck meat during thermal treatment. The results showed that at a CA–DI to MP ratio of 1:500 (g/g) following a 12 min heat treatment, the carbonyl content of MPs in duck meat decreased by 48.30%, and the sulfhydryl content increased by 53.42%. When the concentration was 1:500 (CA-DI, g/g) after 24 min of heat treatment, the •OH and DPPH radical scavenging rates were highest at 59.5% and 94.0%, respectively. And the initial denaturation temperature of MPs was the highest at 96.62 °C, and the thermal absorption was lowest at 200.24 J g⁻¹. At the parameter, the smallest particle size and size distribution range of MP were 190 nm (9.51%). Furthermore, the interplay between CA–DI and MPs contributed to a reduction in the protein particle size and intrinsic fluorescence. In summary, the combination of CA–DI and MPs played a crucial role in inducing protein unfolding and disintegration.