Development of simultaneous nitrification, denitrification and phosphorus removal (SNDPR) is a promising approach for domestic wastewater treatment. Mixed carbon sources by sodium acetate and glucose at various ratios (3:1, 1:1, and 1:3) were investigated to evaluate the effects on the sequencing batch reactors (SBR) based on aerobic granules. Results revealed that the mixed carbon did not change the settleability of aerobic granules, while glucose was more favorable for biomass retention induced by heterotrophs. Both carbon and ammonia nitrogen removal remained unaffected, while increased residual nitrate and phosphorus were detected with higher glucose ratios. Growing percentages of glucose led to more production of extracellular polymeric substances (EPS), especially polysaccharides (PS). Shifts of compositions of EPS were observed by the three-dimensional exaction and emission matrix (3D-EEM) fluorescence spectroscopy. MiSeq pyrosequencing technology demonstrated that the increasing ratios of glucose reduced the diversity of microbial community, though the dominant microbes remained unchanged. Phylogenetic classification of key groups involved in carbon, nitrogen and phosphorus removal suggested that mixed carbon source decidedly shaped the bacterial community.