We aimed to investigate whether vitamin D levels affect the expression of autophagy related genes (Atgs) and the counts of T-cell subsets in active systemic lupus erythematosus (SLE), as well as to assess the association between Atgs and T-cell subsets. Serum levels of 25(OH)D3, Atgs and T-cell subsets were measured in 50 patients with active SLE. Serum 25(OH)D3 levels <10 ng/ml and 10-30 ng/ml were defined as severe vitamin D deficiency and vitamin D insufficiency, respectively. Comparisons were made between values of severe vitamin D deficiency and vitamin D insufficiency patients, and the correlations between Atgs in PBMCs and T-cell subsets were carried out. mTOR mRNA levels were higher (p=0.036) and LC3 mRNA levels were lower (p<0.001) in severe vitamin D deficiency group compared to vitamin D insufficiency group. The counts of CD4+ T cells and the CD4/CD8 ratio were significantly higher in severe vitamin D deficiency group compared to vitamin D insufficiency group (p=0.001, p<0.001,respectively). LC3 mRNA levels correlated negatively with CD4+ T cells counts (r=-0.302, p=0.033), while correlated positively with CD8+ T cells counts (r=0.299, p=0.035). Serum 25(OH)D3 levels correlated negatively with the counts of CD4+ T cells (r=-0.423, p=0.002) and correlated positively with the counts of CD8+ T cells (r=0.318, p=0.024). Our results suggested that severe vitamin D deficiency affected the expression of Atgs in PBMCs and T-cell subsets in active SLE, indicating that vitamin D may affect T-cell subsets via regulating autophagy.