The Jianchang horse (Equus caballus), a famous breed in the southwest regions of China, has excellent mountainous adaptation. The domestic Jianchang horse is popular in China, but information on its origin and evolution is still limited. In this study, we generate complete mitochondrial genome sequences of Jianchang horse. It is 16,614 bp in length, containing 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and and a noncoding control region (D-loop region). And it was found to be similar to other horse mitochondrial genomes. However, there were 105 nucleotide substitutions in the 13 protein-coding genes. The phylogenetic tree analysis was shown that Jianchang horse was significantly clustered as the clade with Debao and Yunnan horse. This genomic data provides useful information for further studies on the genetic diversity and origin of the Jianchang horse population.