Abstract: The water environment pollution caused by acid mine drainage (AMD) has become more prominent in Guizhou. In this paper, an AMD treatment system (using carbonate rock as the reaction medium) of an abandoned coal mine in this area was selected to study the characteristics and functions of the bacterial community structure along the process direction through a high-throughput sequencing technology. The results showed that bacterial community in the system mainly was consisted of Proteobacteria, Chloroflexi and Cyanobacteria. Among of them, Proteobacteria and Chloroflexi were the dominant populations, and 90.95% of Cyanobacteria existed in the suspended matter in the reaction cell. The structure of bacterial community was affected by the concentration of heavy metals in sediment, and the influence of Fe, Ni, As and Pb was especially distinct. There were significant differences in bacterial communities between the front part (inlet and reaction cell) and the back part (sedimentation cell and constructed wetland) of the system. The bacterial α-biodiversity index in sediments increased along the processing flow direction. More than 85% of Fe was removed in multistage reaeration reaction cell. Meanwhile, it was found that iron oxidizing bacteria including Gallionella and Sideroxydans and iron reducing bacteria including Geobacter and Rhodoferax mainly existed in the sediment of the multistage reaeration reaction cell. Additionally, manganese (Mn) in acid wastewater could be removed well through the constructed wetland. Moreover, Pedomicrobium, which could accumulate iron and manganese oxides, was in wetland sediments and plant rhizosphere soil. The abundance of Pedomicrobium (8.38%±1.51%) and Nitrospira (14.75%±0.46%) was higher in constructed wetland than that in multi-stage reoxygenation reaction cell. When the process combining multistage reoxygenation cell with vertical flow constructed wetland with carbonate rock as the main reaction medium was applied to treat AMD, not only carbonate rock neutralization and precipitation but also biological oxidation and biological reduction all played important roles in the removal of pollutants in AMD.