Abstract: In this study, the molecular links between gene expression dynamics and the evolution of Volatile flavor quality during fruiting body development in Morchella sextelata, were investigated. Transcriptome sequencing and gas chromatography-ion mobility spectrometry (GC-IMS) were integrated to identify differentially expressed genes (DEGs) and characterize the volatile profiles at two developmental stages: primordium and fruiting body. A total of 7,120 DEGs were identified, including 3,191 upregulated and 3,929 downregulated genes. Gene Ontology enrichment analysis highlighted oxidoreductase activity, binding activity, membrane-related processes, components of the tricarboxylic acid (TCA) cycle enzyme complex, and carbohydrate/polysaccharide metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated the predominant involvement of ribosome biogenesis, oxidative phosphorylation, pyruvate metabolism, and the TCA cycle. GC-IMS profiling revealed clear stage-specific differences in volatile compounds: ethyl acetate, 3-octanol, and acetoin (3-hydroxy-2-butanone) were most abundant at the primordium stage, whereas phenylacetaldehyde, pentanol, and (E)-2-heptenal were most abundant at the mature fruiting body stage. Correlation analysis showed that alcohols, aldehydes, and ketones were significantly associated with genes related to redox regulation (SOD2 and FXN), amino acid metabolism (ASL), and mitochondrial energy supply (SLC25AL6). Positively correlated genes (GMPS and PPMEL) were associated with the enhanced formation of volatile flavor compounds, whereas negatively correlated genes (BIN3) were associated with the reduced accumulation of putative off-flavor precursors, such as 2-pentanol. These findings provide candidate molecular markers for the quality breeding of M. sextelata and establish a framework for elucidating the gene regulatory networks underlying the biosynthesis of volatile flavors.