Bioethanol production based on solid-state fermentation (SSF) of sweet sorghum stalks has been demonstrated to have great potential due to the its low pollution and low cost. A novel S. cerevisiae strain TSH3 exhibited better SSF performance compared with BY4743 during SSF of sweet sorghum stalks. High-quality total RNA of S. cerevisiae was extracted from SSF mixture and the global gene expression profiles during SSF were studied using RNA-Seq. Compared with BY4743, TSH3's genes related to ribosome biogenesis, amino acid and coenzyme metabolism during early fermentation stage, secondary metabolite biosynthesis, metabolism in diverse environment during middle fermentation stage, and lipid metabolism during late fermentation stage were up regulated; while the genes involved in fatty add metabolism and peroxisome during early fermentation stage, ribosome biogenesis during middle fermentation stage, and mitotic cell cycle during late fermentation stage were down-regulated. Further dynamic analysis of TSH3's transcriptome reveals its three different metabolic stages: 1) ribosome biogenesis and respiration-fermentation transition; 2) biosynthesis of secondary metabolites and stress resistance; 3) plasma membrane related metabolism for stress resistance. These findings provided insight into the S. cerevisiae transcriptome during SSF of sweet sorghum stalks and suggest that TSH3 would be an ideal candidate for SSF-based bioethanol production.