To clarify the molecular mechanism of tetramethylpyrazine (TTMP) synthesis and the flavor regulatory effect of Bacillus siamensis in the solid-state fermentation of Jiangxiangxing Baijiu, B. siamensis strain BQ1004 was isolated from Jiangxiangxing Daqu and was identified by morphological observation and 16S rRNA gene sequencing. Its functional genes were analyzed by whole-genome sequencing. Transcriptome sequencing and bioinformatics analysis were performed on the fermentation broth of the strain at 48, 72 and 108 h (denoted as T48, T72 and T108, respectively), and its impact on flavor substances was evaluated via simulated solid-state fermentation. The results showed that the genome of strain BQ1004 carried complete TTMP synthesis-related enzyme genes, such as those encoding acetolactate synthase and acetolactate decarboxylase. Transcriptome analysis revealed 1716 differentially expressed genes (DEGs) between T48 and T72 (974 up-regulated genes and 742 down-regulated) and 1623 DEGs between T48 and T108 (857 up-regulated genes and 766 down-regulated). Meanwhile, these DEGs were significantly enriched in pathways such as nitrogen metabolism, glycolysis, and oxidative phosphorylation. Among them, alanine, aspartic acid, and glutamic acid provided nitrogen sources for TTMP synthesis by participating in nitrogen metabolism, and key genes such as ald (alanine dehydrogenase) and coxA (oxidative phosphorylation) were up-regulated to drive the rapid synthesis of TTMP. In solid-state fermentation, this strain increased the TTMP content in fermented grains by 189.13% (reaching up to (410.65 ± 13.07) mg/kg) and the total pyrazine content by 139.72%, and also elevated the contents of alcohols, organic acids, and other flavor substances. This study reveals the metabolic mechanism by which B. siamensis regulates the flavor of Jiangxiangxing Baijiu, providing theoretical support for flavor enhancement in Baijiu production.