The current study aimed to investigate the impacts of selenium (Se) treatment on the volatile aroma compounds of broccoli heads, and to understand the underlying mechanisms of aroma substances metabolism. To accomplish this, the dynamic changes of ethylene release rate, respiratory intensity, weight loss rate, and volatile compounds were determined in broccoli heads treated with a 2 mg L−1 sodium selenite solution for 50 days. RNA sequencing (RNA-seq) was conducted on samples taken at 10, 20 and 40 days to uncover the molecular mechanisms of the synthesis and metabolism of aroma substances in broccoli heads. The results showed that Se treatment decreased the release rate of ethylene, respiratory intensity, and weight loss rate. Additionally, an increase in the content of volatile aroma compounds in broccoli heads treated with Se was observed through GC-IMS technique. Aldehydes, esters, and alcohols were found to constitute the majority of these volatile aroma compounds. RNA-seq analysis identified 56,130 transcripts and revealed 524, 1943, and 2274 differentially expressed genes (DEGs) in the Se10d vs. CK10d, Se20d vs. CK20d, and Se40d vs. CK40d groups, respectively. These expression transcripts of volatile aroma substance metabolism were found to be enriched in related pathways, including glycolysis, pyruvate metabolism, fatty acid metabolism, transcription factors, and aromatic amino acid metabolism. In conclusion, this study not only enhances our understanding of selenium's mechanism of action but also has implications for the application of selenium in vegetable preservation.