Streptococcus thermophilus ASCC 1275, a typical dairy starter bacterium that has been completely sequenced, could produce the highest known amount (~1000 mg/L) of exopolysaccharide (EPS) in milk under the optimal condition among the species of Str. thermophilus. However, little is known about the mechanistic insights into the effects of environmental factors such as pH, temperature and whey peptides on its EPS production. In this study, RNA-seq was applied to this organism cultivated in skim milk under different conditions: (1) Cd1 – pH 6.5 and 37°C; (2) Cd2 – pH 5.5 and 37°C; (3) Cd3 – pH 5.5 and 40°C; (3) Cd4 – pH 5.5 and 37°C with whey peptide supplementation. TopHap and Cufflinks pipelines were used for differential gene expression analysis. Results showed that there were 526 genes that have been significantly changed in Cd2 compared with that in Cd1; specifically, ribosomal protein synthesis and EPS assembly genes were significantly upregulated in Cd2 which may explain the enhanced EPS production in Cd2. As for temperature effect, only 49 genes were significantly changed in Cd3 compared with that in Cd2; purine and lactose metabolism were enhanced in Cd3 suggesting that more nucleotide sugars (UDP-glucose and UDP-galactose) may have been synthesized for EPS assembly in Cd3. Whey peptide supplementation induced the significant changes of 16 genes in Cd4 compared with that in Cd2; it was found that cysteine and methionine metabolism and some unidentified amino acid/peptide transporters were improved for bacterial growth fitness. This study indicates that regulation of nucleotide sugar synthesis, EPS assembly and bacterial fitness are responsible for an enhanced EPS production from Str. thermophilus ASCC 1275.