To assess T cell subsets and levels of chemokines and cytokines in patients with SLE and determine their relationships between disease activity and organ involvement. Blood samples from SLE patients (n = 24) and healthy controls (n = 36) were analyzed. Frequency of circulating follicular help T cells (Tfh), central memory T cells (Tcm), effector memory T cells (Tem), and naïve T cell subsets was enumerated and their surface markers expression of inducible T cell co-stimulator (ICOS) and programmed death 1(PD-1) protein was examined by flow cytometry. The disease state in SLE patients was evaluated using the SLE Disease Activity Index (SLEDAI). Concentrations of autoantibodies, serum C-reactive protein (CRP), the erythrocyte sedimentation rate (ESR), lgG, complement 3, complement 4, cytokines, and chemokines, such as IL-21, IL-17A, and IL-1β, were measured. The frequencies of circulating Tfh and Tcm cell subsets were significantly lower than those in healthy controls. However, the percentages of circulating PD1ICOSTfh, PD1ICOSTcm, and PD1ICOSTem of PBMCs from SLE patients were higher than those in healthy controls. Furthermore, increased levels of serum IL-1β, IL-4, IL-6, MCP-1, IL-21, and IL-17A were detected in the patients with SLE compared to healthy controls. In addition, patients with immune thrombocytopenia displayed elevated proportions of serum IL-10, IL-17A, and IL-1β. Aberrant T cell subsets and cytokines expression profile were observed in SLE patients. PD1ICOSTem cell subset was clearly influenced by disease activity and serum IL-10, IL-17A, and IL-1β were significantly increased in patients with immune thrombocytopenia. Therefore, PD1ICOSTem cells might serve as an important tool for recognition and serum IL-10, IL-17A, and IL-1β might be an effective monitor for SLE patients with immune thrombocytopenia.