Flavoromics and metabolomics were used to evaluate the effects of selenium-enriched yeast (SEY) in hen feed on the volatile flavor and nutritional quality indicators in the resulting chicken meats. Volatile organic compounds (VOCs) were analyzed using GC-MS and odor activity value calculations. Ninety-eight VOCs were identified. The treatment group had more abundant VOCs, with mainly increased fat, mushroom, fruit, and vanilla odor. Modulating the nutritional profile of chicken meat through SEY feed can reduce saturated fatty acid levels, increase unsaturated fatty acid levels, and significantly reduce cholesterol levels in Dongxiang green-shell chicken (DX). Metabolomics analysis has elucidated the potential mechanisms, whereby adding SEY to the diet of DX reduces cholesterol levels through secondary bile acid biosynthesis pathways. Its related metabolic changes may also directly or indirectly promote the formation of key substances that give meat its flavor. Adding SEY to the diet of Jingfen laying hens affects the muscle metabolism environment via the propanoate metabolism pathway, increasing the grassy notes of chicken meat while reducing its gamey taste.