Gallic acid is a natural phenolic acid that has a stress inhibition effect on Escherichia coli. This study elucidates the physiological mechanism of E. coli 3110 response to gallic acid by integrating fermentation characteristics and transcriptional analysis. Compared with the control (without stress), the cell growth was severely inhibited, and irregular cell morphology appeared in the case of high levels of gallic acid stress. With the increase of gallic acid content in the fermentation medium, the glucose consumption of E. coli decreased successively. Moreover, cofactor levels (ATP, NAD+ and NADH) of E. coli 3110 were also lowered under gallic acid after 20 h stress, indicating a stronger inhibitory effect of gallic acid on E. coli. The transcriptional analysis revealed that gallic acid altered the gene expression profiles related to five notable differentially regulated pathways. The genes related to the two-component system were up-regulated, while the genes associated with ABC-transporter, energy metabolism, carbon metabolism, and fatty acid biosynthesis were down-regulated. This is the first report on the systematic evaluation of the toxicity of gallic acid on E. coli. This study has a guiding significance for the efficient production of phenolic compounds by E. coli and provides new ideas for the study of microbial tolerance to environmental stress and the discovery of related tolerance targets.