The effect of ibuprofen (IBU) on the sulfur autotrophic denitrification (SAD) process and microbial toxic response mechanism were investigated. Nitrate removal performance was inhibited by high IBU concentrations (10 and 50 mg/L), and the effect of low IBU concentrations (1 mg/L) on nitrate removal performance was negligible. The low IBU concentration induced basal oxidative stress for microbial self-protection, while the high IBU concentration induced high-intensity oxidative stress to damage the microbial cell membrane structure. Electrochemical characterization showed that the low IBU concentration stimulated the electron transfer efficiency, which was inhibited at the high IBU concentration. Moreover, the variation content of nicotinamide adenine dinucleotide (NADH) and nitrate reductase showed that metabolic activity increased at low IBU concentrations and decreased at high IBU concentrations during the sulfur autotrophic nitrate reduction process. This study proposed the hormesis toxic response mechanism of the SAD process to IBU exposure.