This research used BFT to feed larvae with an initial weight of (15.35±10.62) mg for 37 days at a feeding density of 5 000 tail/m³ to investigate the effect of biofloc technology (BFT) on the growth of GIFT Oreochromis niloticus larvae and its relationship with gut microbiota. A survival rate of (65.08±13.55)% and a final density of (3 254±678) tail/m³ were obtained at the end of the experiment. The body weight of fry in class B (0.1-0.2 g) was the most, which was significantly higher than that of the other four classes (0<A≤0.1 g，0.2 g<C≤0.3 g，0.3 g<D≤0.4 g，0.4 g<E). Proteobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, and Firmicutes were the dominant phyla in the five grades of larvae. Among the dominant genera of intestinal flora, probiotics such as Bacillus (3.17%-5.32%), Rhodibacter (1.91%-3.26%), Reyranella (1.90%-2.62%) were detected. There were also some potential pathogens at the same time, such as Flavobacterium (4.98%-9.20%), Enterovibrio (0.21%-6.47%), Mycobacterium (2.16%-4.37%), Aeromonas (0.29%-1.10%). The relative abundance of Aeromonas and Enterovibrio was higher in the lower weight class. The health status and growth rate of larval tilapia were affected by intestinal probiotics and potential pathogenic bacteria. However, excessive pathogenic bacteria might break the balance of bacterial flora and further affect the growth rate of GIFT O. niloticus. The results of this study illustrated the possible relationship between the growth rate of GIFT O. niloticus larvae and the gut microbiota, and provided a reference for the cultivation of GIFT O. niloticus larvae by BFT.