Nitrate and phenol often co-occur in wastewater because of the complex industrial and agricultural processes, while the impacts of phenol on autotrophic denitrification remain unclear. Here, a sulfur and hydrogen-oxidizing autotrophic denitrification reactor was established, and the effects of different concentrations of phenol on the nitrate removal performance, kinetics, microbial communities, and functional genes were investigated. Increasing concentrations of phenol significantly decreased the denitrification efficiency in the reactor. The kinetic data indicate the limitation of nitrate diffusion may be one of reasons. Increasing phenol concentrations declined the activities of nitrate and nitrite reductases and induced the production of reactive oxygen species (ROS) and the release of lactate dehydrogenase (LDH), suggesting potential toxicity to the denitrifying consortium. Denitrifying gene nirK was most sensitive to phenol stresses in the reactor. In addition, Thauera was the predominant genus in system with and without phenol, Bacillus was enriched under high phenol concentrations.