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The interaction between nutrients, heavy metals, and sediment bacterial communities play a key role in the health of crabs and the biogeochemical cycles of aquaculture systems. However, the effects of sediment improvement activities in crab culture on nutrients and heavy metals and the response of bacterial communities to the relevant changes are unclear. In this study, 24 water and sediment samples were collected from two aquaculture sites (total of 12 ponds, 6 at each site). High-throughput sequencing was used to determine the structure of the bacterial community and the diversity in water and sediment samples. The relationship between nutrients, heavy metals, and bacterial communities and the changes of the three before and after the improvement of the sediment were analyzed. The results showed that Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Firmicutes were predominant at the phylum level of sediment. Sediment improvement has an effect on NH4+-N, sulfide, total organic carbon (TOC), and heavy metals in sediments to varying degrees. In addition, redundancy analysis found that NH4+-N, NO3−-N, TP, and heavy metals were key drivers in crab culture pond sediments. The results of functional prediction showed that carbon, nitrogen, and sulfur metabolism were the dominant processes in the two crab farming areas. Overall, changes in nutrients and heavy metals caused by sediment improvement further affected the structure and function of bacterial communities and may affect biogeochemical cycles. Our study has deepened the understanding of the effects of sediment improvement on nutrients, heavy metals, and bacterial communities in crab culture ponds. [ABSTRACT FROM AUTHOR]