Egg yolk forms have several health and industrial applications, but their storage characteristics and gel mechanisms have not been thoroughly studied. In order to investigate the relationship between the changes in structure and properties of egg yolk gel and egg yolk powder during storage, in this paper, egg yolk powder was stored at 37 °C for 0, 1, 3, and 6 months in an accelerated storage experiment, and the influence of storage time on the gel properties of egg yolk powder was analyzed. The results showed that the contents of protein carbonylation and sulfhydryl in the yolk decreased gradually with the extension of storage time. Circular dichroism and fluorescence spectra showed that the ordered structure and structural stability of egg yolk proteins decreased gradually. Oxidation led to the formation of intermolecular crosslinking in the egg yolk proteins and oxidized aggregates, resulting in a decrease in surface hydrophobicity, which affected the gel properties of the egg yolk powder after rehydration, resulting in the phenomenon of lipid migration and gel degradation. The results provide a theoretical basis for improving egg yolk powder’s overall quality and storage stability.