Objective To explore the relationship between gut microbiota and anti-dsDNA antibody in systemic lupus erythematosus (lupus) TC mice. Methods ELISA was performed to detect serum anti-dsDNA antibody in the lupus TC mice. Then, the feces of both dsDNA-positive and -negative mice were collected, and 16S rRNA of the stool sample was sequenced by Illumina HiSeq 2500 high-throughput sequencing, to analyze the relationship between gut microbiota and anti-dsDNA antibody level in the two groups. Results The result of ELISA and mouse fecal high-throughput sequencing showed that the species diversity of gut microbiota in the dsDNA-positive TC mice was significantly lower than that in the dsDNA-negative TC mice. The gut microbiota of TC mice in the two groups showed significant differences at different classification levels: Chloroflexi at phylum level, Betaproteobacteria, Deltaproteobacteria and Ktedonobacteria at class level, Burkholderiales, Desulfovibrionales and Ktedonobacterales at order level, Alcaligenaceae and Desulfovibrionaceae at family level, and Parasutterella and Desulfovibrio at genus level ( P <0.05 for all). Conclusions The flora composition of gut microbiota in lupus TC mice is highly correlated with anti-dsDNA antibody. The results of our study provide a basis for further elucidation of the relationship between gut microbiota and the pathogenetic mechanism of systemic lupus erythematosus.