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Application of biofloc technology could effectively treat wastewater. However, the effect of influent carbon to nitrogen ratio (C/N ratio) on water quality and microbial community structure evolution in suspended growth bioreactors (SGBRs) through biofloc technology is still unclear. Here, we show that the total ammonia nitrogen (TAN) and nitrite nitrogen in the effluent of the C/N 10 treatment was significantly higher than that in the C/N 15, C/N 20 and C/N 25 treatments (p < 0.05). Higher TAN removal efficiency was obtained in treatments of C/N 15, C/N 20 and C/N 25, and there was no accumulation of nitrite nitrogen and nitrate nitrogen. Increasing the C/N ratio strengthened the elimination ability of total phosphorus and chemical oxygen demand (COD). The concentrations of TAN and COD first dropped to the lowest level and then increased slightly within one cycle in all treatments. The accumulation of biomass in the reactors increased with the increasing C/N ratio, indicating that a higher C/N ratio was conducive to microbial proliferation. The 16S rRNA sequencing revealed that the microbial community diversity in SGBRs was significantly higher than that in the natural wastewater (P0). The predominant phylum were Proteobacteria, Bacteroidetes and Verrucomicrobia, but Saccharibacteria occupied a dominant position in the late period of the experiment. Pathogens, such as Aeromonas, Acidovorax, Flavobacterium, and Malikia were significantly decreased after high C/N ratio simulative wastewater treating natural wastewater in the reactors. In summary, the water quality and biomass concentrations in SGBRs can be improved under the conditions of influent C/N ratio, equal to or greater than 15.