In this study, sediment cores were collected in Meiliang Bay, Lake Taihu. The surface 50 mm sediment were sliced at 2 mm section using the self-made device to analyze the vertical distribution of bacterial communities in sediment with high-throughput sequencing technology. High-resolution dialysis and diffusive gradients in thin films technology (DGT) with resolution of millimeter were used to analyze the vertical distribution of dissolved and DGT-labile ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), Fe and P. Results indicated that the composition of bacterial community, concentrations of dissolved and DGT-labile NH₄⁺-N, NO₃^--N, Fe and P changed significantly across the sediment depth. Bacterial nitrate reduction process mainly occurred at the sediment depth from -16 mm to 0 mm, which should cause an obvious decrease in the concentrations of dissolved and DGT-labile NO₃^--N in this sediment depth. Bacterial iron reduction process mainly distributed in the sediment depth from -32 mm to -18 mm, while bacterial sulfate reduction process mainly dominated in the sediment depth from -50 mm to -34 mm. Bacterial sulfate reduction was the main cause for the significant increase of dissolved and DGT-labile Fe and P concentrations in the sediment depth from -32 mm. This study has deepened the understanding of the bacterial influence on the vertical migration and transformation of nitrogen and phosphorus in eutrophic lake sediments.