In this study, Beijing duck breast myosin was used to analyze the structural and functional changes during thermal treatments. The particle size and atomic force microscopy (AFM) imaging results showed that the myosin polymer formed generously at 55 °C. Meanwhile, the myosin denatured and unfolded at 50–55 °C leading to the exposure of hydrophobic groups detected by structural determinations including circular dichroism (CD), sulfhydryl content and Ca2+-ATPase activity. The increase of hydrophobic interaction was observed to promote the myosin aggregation at 55 °C, and disulfide bonds played a supplementary role in the stabilization of myosin aggregates at 80 °C. Molecular docking and dynamics simulation verified that electrostatic energy of myosin decreased on reaching 55 °C, and the hydrophobicity increased to promote the aggregation while kinetic energy increased at 80 °C. The presented study provided a potential selection of processing temperature conditions from the aggregation of protein.