The impact of processing on the protein degradation and quality of emulsion sausages was studied. Analysis of SDS-PAGE, water-soluble nitrogen, and non-protein nitrogen showed processing affected protein degradation, and the degree of degradation was increased with increasing cooking temperatures. The significant increase of Tyr, Lys, Cys, Asp and Glu as free amino acids content confirmed the protein degradation during processing. Color and texture parameters showed significant changes with processing. Sausages (90 °C) had more flower, green, and fruity flavors, while sausages at 120 °C had more oil, fat, and warm flavors. Pearson correlation analysis showed that protein degradation had a significant effect on the quality of emulsion sausages during processing. The changes in morphology of water-soluble and salt-soluble proteins can explain the protein turbidity and texture changes at a microscopic level during processing. Furthermore, a label-free strategy was used to investigate the changes in the proteomes between 0 and 120 °C sausages. Differentially expressed proteins, and disappearing and emerging proteins affected the quality of sausages directly or indirectly. These proteins could be regarded as important factors affecting sausages.