In order to understand the operating effects of the nitrification and heterotrophic biofloc culture systems, the experiment was conducted to culture GIFT Oreochromis niloticus juveniles in the nitrification group and the heterotrophic group for 51 days, and to compare the growth performance and non-specific immune enzyme activity, digestive enzyme activity of tilapia, and community structure of water and intestinal microorganisms. The results showed that there was no significant difference in the growth performance indicators such as survival rate and weight gain rate of the two groups of tilapia. The non-specific immune enzyme activity of the heterotrophic group tilapia was significantly higher than that of the nitrification group. The activities of amylase and lipase in the intestine of tilapia in the nitrification group were significantly higher than those in the heterotrophic group, and the protease in the heterotrophic group was significantly higher than that in the nitrification group. The top 5 dominant phyla of tilapia intestines are Proteobacteria, Actinobacteria, Chloroflexi, Firmicutes and Chlamydiae. Among them, the Proteobacteria phylum is the most important flora in each group. The top 4 dominant phyla in the water of the nitrification group are Proteobacteria, Chloroflexus, Bacteroidetes, and Planctomycetes; the top 4 dominant phyla in the water of the heterotrophic group are Proteobacteria, Chloroflexus, Bacteroides, and Actinomycetes. Mycobacterium is the most important potential pathogenic bacteria in water and intestinal tract, while Diplorickettsiaceae and Plesiomonas maintained at a low level. Except for Clostridium, other potential pathogenic bacteria such as Aeromonas and Flavobacterium in the water and intestines were higher in the nitrifying group than in the heterotrophic group.Through the comparison of the cultivation effect, fish biochemical indexes and intestinal microorganisms, it was found that heterotrophic bioflocs were more beneficial to the cultivation of juvenile tilapia.