We sought to analyse the expression characteristics of cytochrome C oxidase subunit I in mitochondrial of MRL/lpr lupus mice. The whole blood of MRL/lpr lupus mice was detected for whole mitochondrial genome sequencing performed by Illumina HiSeq PE150 instrument, compared with house mouse (NC_005089.1) and screened for the maximum difference gene, MT-CO1. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot were used to detect the mRNA and protein expression of MT-CO1 in lupus mice and control mice. The total antioxidant capacities of lupus mice and control mice were measured using the rapid 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) method. The mitochondrial genome sequencing showed that five mitochondrial genes had base differences and MT-CO1 was the maximum difference gene, 31 in total. Among the 31 base difference sites, 2 were missense mutations and 29 were synonymous_variant. qRT-PCR test results showed that the MT-CO1 expression in lupus mouse blood was statistically lower than that in control mice blood (t=4.333; p=0.0003). Western blot test results revealed that the expression of MT-CO1 was lower in the lupus mice compared with the control mice at the protein level. Serum total antioxidant capacity testing showed that: the serum total antioxidant capacity of lupus mice was statistically lower than that of the control mice (t=9.957; p<0.0001). High mutation rate and decreased expression of MT-CO1 in MRL/lpr lupus mice accompanied the decrease of antioxidant capacity, which indicated that abnormal MT-CO1 might be involved in the pathogenesis of SLE and the production of anti-dsDNA antibodies.