In view of the difficulties of treating acid mine drainage (AMD), the formation mechanism of AMD was introduced. The species and functions of prokaryotes and eukaryotes in AMD were discussed, and the application examples of microbial remediation technology were summarized. The analysis showed that biological oxidation dominated by microorganisms was the main reason for accelerated oxidation of AMD. Prokaryotes such as archaea and bacteria oxidized mineral elements in mine water, and some eukaryotes such as protozoa, algae and fungi could slow down the pollution in AMD. Making full use of the physiological metabolism of microorganisms could strengthen the repair effect. Bioremediation technology combined with source control and end treatment was an important direction of future research.