Influence of pH on the dominant microbial community structure in bioelectrochemical system (BES) for nitrate removal is poorly understood. Here, the dynamics and variations of microbial communities were investigated with pH varied from 6.0 to 9.0 in a novel three-dimensional BES (3D-BES). The maximum nitrate removal efficiencies 97.58 and 96.36 % were obtained at pH 7.0 and 8.0, due to the main contributions of bacterial phylum Firmicutes and class Clostridia. The abundances of dominant phyla and classes tended to decrease under pH 6.0 and 9.0 conditions. Additionally, phylum Proteobacteria and class Gammaproteobacteria preferred acid environment in the BES, while phylum Chloroflexi and class Bacilli and Betaproteobacteria preferred alkaline environment. Furthermore, the excellent nitrate removal ability of the 3D-BES was ascribed to the presences of genera Exiguobacterium, Proteiniclasticum, Pseudomonas, Planococcus, Thauera, Azoarcus, Thiobacillus, etc. These genera facilitated the combined autotrophic denitrification process so that this system achieved excellent nitrate degradation efficiency.