The research focused on the distinctive empty cup aroma, with the aim of identifying the key aroma compounds and the formation mechanism of empty cup aroma in soy sauce aroma type baijiu (SSB). The lasting times of SSB is significantly longer than that of other types of baijiu, with an average duration of 28 days. Key compounds such as 2,3-dimethyl-5-ethylpyrazine, phenylethyl alcohol, p-cresol, sotolon, benzeneacetic acid were identified in empty cup aroma due to their highest flavor dilution factor. Molecular dynamics (MD) simulation was performed to study the mechanism of empty cup aroma on the liquid−gas interface and solid−gas interface. The results revealed the existence of hydrogen bonding and van der Waals forces between sotolon and lactic acid, a representative nonvolatile compound, which are speculated to be an important reason for the empty cup aroma.