Objective To investigate the correlation between the distribution of critical differential bacterial populations and lymphocyte subsets in systemic lupus erythematosus （SLE） patients by detecting the abundance changes of intestinal microbiota and lymphocyte subsets. Methods Twenty-three SLE patients and 16 healthy controls (HC) were included. Flow cytometry was used to detect the number of peripheral blood lymphocyte subsets, and 16S rRNA technology was used to detect the diversity and abundance of intestinal microbiota. The correlation between peripheral blood lymphocyte subsets and intestinal microbiota was investigated, and the experimental data were analyzed using SPSS 26.0. Results Compared with HC, the numbers of regulatory T（Treg） cells, initial CD4⁺T cells, and interferon（IFN）γ-secreting γδT cells in SLE patients were significantly reduced (t=-2.284, P=0.022; t=-2.084, P=0.037; t=-2.370, P=0.017), and follicular regulatory T （Tfr）, follicular helper T （Tfh）, germinal center B （GC-B）and B lymphocytes showed a downward trend. The relative abundance of Firmicutes in SLE patients was significantly decreased (t=-2.323, P=0.020) and was positively correlated with Tfr (r=0.544, P=0.029) and GC-B cells (r=0.518, P=0.040). The abundance of Bacteroidetes was positively correlated with Tfr cells (r=0.521, P=0.039). Conclusions The peripheral blood lymphocyte subsets and intestinal microbiota levels of SLE patients are significantly different from those of HC, there was a correlation between the intestinal flora and lymphocyte subpopulations in the intestinal tract of SLE patients, especially the Firmicutes and Bacteroidetes are positively correlated with Tfr, Tfh and GC-B cells, suggesting that the structural changes of intestinal microbiota may affect lymphocyte subsets and mediate the progression of the disease.