High concentration of nitrate was widespread in industrial and agricultural effluents, while the impact of phenol as a co-contaminant on denitrification activity and microbial community remained unclear. Here, an expanded granular sludge bed (EGSB) reactor was continuously operated to treat high-nitrate wastewater with increasing phenol stress. The 454 pyrosequencing technology and quantitative polymerase chain reaction (qPCR) were applied to analyze microbial community shift and dynamics of denitrifying functional genes, respectively. Complete denitrification was achieved at 600 mg/L influent phenol stress, while the removal of nitrate decreased to below 82% and nitrite started to accumulate in the effluent when influent phenol exceeded 800 mg/L. The biodiversity and richness of microbial community experienced U-shaped process, and showed significant increases when EGSB reactor turned into crash under 800 mg/L phenol. The 454 pyrosequencing and statistical analyses revealed that Denitromonas was the most dominant denitrifier with a high abundance over 67% in bacterial community and significantly positive correlated with napA gene and nosZ gene, indicating Denitromonas was mainly responsible for the high nitrate removal. And other denitrifiers including Halomonas, Pseudomonas and Parococcus increased along with phenol, that would also act as crucial phenol-resistant denitrifiers under higher phenol stress. This study will not only extend our knowledge regarding biological denitrification under phenol stress, but also could be technically useful for regulation and optimization of the biological treatment processes of the industrial wastewater containing high concentrations of nitrate and phenol.