Objective This study aimed to clone the CDS region of cathepsin K (CTSK) from Guangxi Bama mini-pig and analyze its genetic structure with bioinformatics software. Methods Total RNA was extracted from subcutaneous fat tissue of a Guangxi Bama mini-pig. The CTSK gene CDS region sequence was obtained through RT-PCR.Its sequence characteristics, evolution, encoded protein structure and physical and chemical properties were analyzed using relevant bioinformatics softwares. Results The CDS of the CTSK gene of Guangxi Bama mini-pig was 993 bp and encoded 330 amino acids, which was completely consistent with the published CTSK gene sequence of pig (NM_214302. 1) on NCBI. Homology comparison showed that the CTSK gene has been highly conserved during evolution. The CTSK protein of Guangxi Bama mini-pig had an obvious hydrophilic region and a signal peptide sequence in the region of amino acids 17-330, but had no transmembrane structural domain. Structural prediction indicated that there were two n-glycosylation sites in the CTSK protein, and subcellular localization analysis indicated that it was mainly distributed in the endoplasmic reticulum and nucleus. Conclusions In this study, the CDS region sequence of the CTSK gene in Guangxi Bama mini-pig is successfully cloned and analyzed, which provides a theoretical basis for further study on the function of this gene and the establishment of animal models of related diseases.