Numerous immune cell types, such as B and T lymphocytes, natural killer cells (NK), and NKT cells, are related to the pathogenesis of diseases in systemic lupus erythematosus (SLE). Our goal in this investigation is to examine the phenotype of NK cells and NKT cells alterations in individuals with SLE. Typically, 50 SLE patients and 24 age-matched healthy people had their PBMCs obtained. Employing flow cytometry, the phenotype of NK and NKT cells and immunoglobulin-like transcript 2 (ILT2) expressions were identified. ELISA was utilized to evaluate the amounts of interleukin-15 (IL-15) and sHLA-G in the serum. The frequencies of the circulating NK and NKT cells in individuals with SLE were decreased compared to healthy controls. Furthermore, ILT2 expression was significantly increased in NKT cells, but showed no obvious change in NK cells. Clinical severity and active nephritis were substantially associated with ILT2+ NKT cell frequencies. The correlation study showed that the upregulation of ILT2 expression was related to sHLA-G in plasma but not to IL-15. ILT2+ NKT cells have a vital function in the immune abnormalities of SLE, which can also supply a viable goal for therapeutic intervention. Key Points •ILT2 expression was significantly increased in NKT cells in SLE patients. •ILT2+ NKT cell frequencies were associated with clinical severity which may be used as an indicator for evaluating disease activity in patients with SLE.