Abstract: The microbial abundance and diversity of sponge iron filler in different height of BAF reactor were analyzed and studied by polymeraes chain reaction(PCR) amplification of the target fragment, Illumina high-throughput sequencing and biological information analysis. The results show that the dominant species in the raw Ctrl (raw water) and the reactor were mainly Proteobacteria, followed by Bacteroidetes. In Rank-Abundance distribution curve, the number of Ctrl species is 1 193, while that of DO1 (BAF upper), DO2 (BAF middle) and DO3 (BAF lower) is 2 389, 2 211 and 1 890, respectively, and DO1 has the highest abundance and species diversity. In the reactor, with the decrease of DO (or the decrease of filler spatial position), the richness and diversity of microbial community decreased gradually. It is found that the Chao1 index is more sensitive to the species richness than the observed species index, and the measured number of operational taxonomic units (OTUs) is about 400 higher. DO1 and DO2 samples had higher homogeneity, and the proportion of dominant bacteria in DO3 and Ctrl samples was high and the homogeneity was low. The species composition of DO1 and DO2 was observed to be most similar by PCoA.