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In this study, the flavor characteristics and physicochemical properties of salted egg yolk (SEY) under different cooking methods (steaming/baking/microwaving) were investigated. The microwave-treated SEY exhibited the highest levels of salt content, cooking loss, lightness, and b* value, as well as the highest content of flavor amino acids. A total of 31, 27, and 29 volatile compounds were detected after steaming, baking, and microwave treatments, respectively, covering 10 chemical families. The partial least squares discriminant analysis confirmed that 21 compounds, including octanol, pyrazine, 2-pentyl-furan, and 1-octen-3-ol, were the key volatile compounds affecting the classification of SEY aroma. The electronic nose revealed a sharp distinction in the overall flavor profile of SEY with varying heat treatments. However, no dramatic differences were observed in terms of fatty acid composition. Microwave treatment was identified as presenting a promising approach for enhancing the aroma profile of SEY. These findings contribute novel insights into flavor evaluation and the development of egg products as ingredients for thermal processing.