Abstract: To explore the distribution of microbial communities in different functional zones of coal mine and their response to hydrogeochemical characteristics, a coal mine in Ordos was taken as the research object. 24 water samples were collected from six typical functional zones involved in the whole process of the mine water source, formation, collection and discharge. Hydrochemical components detection and high-throughput sequencing of microbial 16S rRNA genes were carried out. and multivariate statistical methods were used for sequence data processing. The results showed that the hydrochemical type of mine water was high salinity SO₄-Na type, which directly inherited the supplied water-source, while the concentration of characteristic pollutant\rmSO_4^2 - was highest in coal roadways and surface water pools. The compositions of microbial communities in different functional zones presented significant differences. The dominant bacterial genera detected at the genus level includedThiothrixand sulfur oxidizing bacteria that could oxidize sulfides (i.e.,ThiothrixandSulfuricurvum), as well as newSphingobacteriaandShortwave Monocmonasthat can degrade organic matter (i.e.,NovosphingobiumandBrevundimonas), while they distributed relatively high in coal tunnels and goafs. The abundances of aerobicUliginosibacteriumandAcinetobacterwith strong adsorption and organic degradation, was highest in rock roadways. Bacteria related to nitrogen cycle (i.e.,HydrogenophagaandRhodobacter) accounted for the higher proportion in water sumps and surface water. Microbial communities were sensitive and closely related to the hydro-chemical processes. The distribution of microbial communities in underground coal mine was not only related to nutrients such as C, N, Ca and Mg, but also closely interrelated to redox sensitive substances such as Fe, COD and\rmSO_4^2 - . Coal roadways and goafs are the key zones for groundwater pollution prevention and control. After mining disturbance, the low valent sulfides associated with coal have generated a large amount of\rmSO_4^2 - through the chemical oxidation and catalytic oxidation of sulfur oxidizing bacteria. However, it is worth noting that when the working pannel stopped for six months to three years, the characteristic pollutant\rmSO_4^2 - was reduced by 15%-34% due to the physical or chemical adsorption, precipitation (dominated in the early stage), and the reduction of sulfate reducing bacteria (dominated in the later stage). This result indicated that the goaf had a certain degree of self-cleaning ability. In summary, the research results could provide theoretical supports for the engineering applications of mine water pollution prevention and control, which was reflected in the following two aspects: on the one hand, to reduce the generation of\rmSO_4^2 - from the source by maintaining the anaerobic condition on the working pannel through nitrogen gas supply; on the other hand, after screening and cultivating the sulfate-reducing bacteria and organic matter degrading bacteria, they would be produced into bio materials, and added to the underground for in-situ remediation of groundwater pollution.