Acid mine drainage (AMD), with low pH values and high concentrations of metals (e.g. Fe, Mn), is a common problem caused by the oxidation of sulphide minerals, posing seriously risk to surrounding environment in areas of the southwest China. Previous studies have confirmed that acidophilc bacterias play an important role in the generation of AMD and remediation of AMD, but few researches has been done on the in-situ remediation of AMD in field and little attention has been paid to the variations of microbial community composition in such an AMD treatment system. A pilot system consisting of two oxidation-precipitation cells, two microbial treatment cells and one setting cell, based on microbiological technology, was constructed to treat AMD, and has been effectively running over 5 years up to now. However, we still didn’t know what kind of the microbial community compositions stay in and how they work in the different cells of the pilot system. 48 Sediment samples from different treatment cells in different seasons were collected, and the microbial community compositions in samples were extracted and analysed the Illumina MiSeq platform at Novogene bioinformatics company (Beijing, China). The results showed that the concentrations of Fe, Mn and SO₄^2- were reduced from 920, 46 and 4905 mg/L (inflow) to 71.6, 12 and 3436mg/L (outflow), with the removal rates are 92% for Fe, 73% for Mn, and 29.9% for SO₄^2-, respectively. The increase in pH and decrease of oxidation-reduction potential (Eh) were also observed along the water flow direction in the system. We also found Ferrovum, Metallibacterium, and Leptospirillum were highly enriched in the pilot cells. Meanwhile, Canonical Correlation Analysis (CCA) results indicated pH, TS and Amorphous iron oxide were significantly correlated with the overall microbial communities. And the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree indicated that distinct microbial communities developed within this pilot system in different time. Based on PCoA (Principal Coordinates Analysis), the microbial composition of each cell was distinct, indicating the physicochemical parameters including pH, TS and Amorphous iron oxide had remarkable effects on shaping the indigenous microbial communities. In conclusion, it was documented that the pilot system is an appropriate system for coal AMD remediation, and the significant differences of microbial community composition were found in different cells of this system and in different seasons.