[Objective] To investigate the adaptive mechanism of bioleaching microorganisms to extreme environment based on CRISPR system at the genomic level, bioinformatic analyses were performed on the structural characteristics and homology of CRISPR-Cas system in genomes of 100 species from genera (Acidithiobacillus, Desulfovibrio, Leptospirillum, Sulfobacillus, Acidiplasma and Ferroplasma) in acid mine environment. [Methods] We downloaded genome sequences from NCBI website and identified potential CRISPR arrays by using CRISPR Finder. The composition, structure and function of each CRISPR system were analyzed, where repeats were classified by Clustal Omega and spacers were aligned and annotated according to nr database, plasmid database and viral database, respectively. The CRISPR-Cas system of microorganisms in acid mine environment was classified based on the types and homology of Cas proteins. [Results] Among the genomes of 100 bioleaching microorganisms, we found 415 CRISPR arrays. There were 80 different repeats and 4147 spacers in 176 confirmed CRISPR arrays. All the 12 types of repeat sequences in each cluster could form typical RNA secondary structure and the sequence of cluster 10 was the most representative one among all the bioleaching microorganisms. The annotation results showed that these microorganisms have been attacked by bacterial plasmids and virus, and have resisted the invasion of foreign nucleic acid sequences through different defense mechanisms. Most of the CRISPR-Cas systems of bioleaching bacteria belong to I-C and I-E subtypes, while most of the CRISPR-Cas systems of archaea belong to I-D subtype. There are significant differences between them in the evolution process based on the CRISPR-Cas system. [Conclusion] The CRISPR structure of acid mine environment microorganisms may mediate the interaction between foreign nucleic acid sequence and Cas protein based on different immune mechanisms, which provides a foundation for further revealing the adaptive evolution mechanism of extreme environment microorganisms.