Abstract: The aim of this study was to illuminate the role of the Cmr3 of Ⅲ-B CRISPR-Cas system of Thermoanaerobacter tengcongensis in thermal adaptation. The cmr3 was cloned by PCR, and constructed to the prokaryotic expression vector, which was transformed into Escherichia coil. The Cmr3 protein was expressed after induced.Applying bioinformatic software to analyzing comparable basic physiochemical properties and tertiary structure of cmr3 gene encoded amino acids in Thermoanaerobacter tengcongensis and two mesophiles. The results showed that:Cmr3 of T. tengcongensis was expressed in E. coli. The molecular mass is 43.4 kDa; bioinformatics analysis showed that the length of cmr3 gene was 1 134 bp, encoding 337 amino acids. The Cmr3 protein is hydrophilic. In comparison, T. tengcongensis has higher thermos ability than mesophiles, and the tertiary structure was more compact than mesophiles. The results of this study provide scientific basis for the study of the process of thermal adaptation in the CRISPR-Cas system of thermophiles.