To investigate the effects of different oligosaccharides on the formation of biofloc and the structural characteristics of biofloc flora. Using glucose (GLU) as control, xylo-oligosaccharides (XOS), fructooligosaccharides (FOS), mannan-oligosaccharides (MOS), soybean oligosaccharides (SBOS), and maltose oligosaccharides (MTOS) were used as carbon sources to culture biofloc, ammonium chloride was used as nitrogen source and C/N was 15. The results showed that suspended particulate matter content and biofloc volume in the SBOS group were significantly increased (P<0.05) compared with other groups, and there were no significant differences between other oligosaccharide groups and the control group (P>0.05). Ammonia nitrogen gradually decreased and then stabilized. Compared with the control group and other experimental groups, the level of ammonia nitrogen in the SBOS group was significantly decreased (P<0.05). Except for the FOS group, the ability to reduce ammonia nitrogen in other experimental groups was higher than that in the control group. There was no significant difference in nitrite nitrogen degradation (P>0.05). Nitrate nitrogen showed a trend of decrease first and then increased, and the accumulation of nitrate nitrogen was decreased in all groups except the XOS group, and the accumulation of nitrate nitrogen was significantly decreased in the SBOS group and MTOS group (P<0.05). Compared with the control group, the abundance of biofloc and microbial diversity index was significantly decreased in the XOS group (P<0.05). From the analysis of phyla level, proteobacteria had the highest abundance in all experimental groups. Compared with the control group, proteobacteria and Proteobacteria in oligosaccharide groups were improved, and the abundance of Proteobacteria and Bacteroidetes in the FOS group was significantly increased (P<0.05). Regarding subordinate level, the proportion of Bdellovibrio decreased in the experimental group compared with the control group (P>0.05). Compared with the control group and other experimental groups, the FOS group significantly increased the abundance of unclassified_f_Rhodobacteraceae and significantly decreased the abundance of unclassified_f_Rhodobacteraceae and norank_f_Enterobacteriaceae (P<0.05). The results show that the biofloc constructed by oligosaccharide as carbon source can improve water quality, optimize bacterial community structure, increase the number of beneficial bacteria, and reduce the number of harmful bacteria. This study provides some theoretical basis for applying of oligosaccharides as carbon source in biofloc.