epsilon-Poly-L-lysine (epsilon-PL), a natural food preservative, is mainly produced by Streptomyces in aerobic fermentation. Previously, we have significantly enhanced epsilon-PL production through a pH shock strategy. To understand the underlying reason between pH shock and high epsilon-PL production, RNA-seq technology was conducted in this study to investigate the temporal transcription at three time-points corresponding to early, mid-term and late stages of fermentation. Transcription of genes related to signal transduction, electron respiratory chain, membrane transport, nitrogen metabolism, energy metabolism and redox homeostasis were significantly up-regulated, accompanied by the increase of intracellular ATP, respiratory activity. The assay of intracellular reactive oxygen species and malonaldehyde showed that pH shock could enhance the antioxidant capacity and reduce oxidative damage of cells effectively. We deduced that signal transduction systems play a major role in responding to pH shock, and result in the enhancement of the metabolic vitality and intracellular redox homeostasis. The obtained information will facilitate future studies for epsilon-PL production improvement and lay a foundation for molecular mechanism investigation of pH shock.