To observe the efficacy of umbilical cord mesenchymal stem cells (UC-MSCs) transplantation for the patients with refractory systemic lupus erythematosus (SLE).Thirty seven patients with SLE were enrolled in this study, and divided into conventional treatment group (control group, n = 20) and UC-MSCS adjuvant treatment group (treatment group, n= 17). All the patients in both two groups were treated with glucocorticoids and cyclophosphamide (CTX). In the UC-MSCs group, each patient additionally received the transplantation of 3 x 10(7) UC-MSCs infusion intravenously. The clinical manifestations and laboratory parameters of each patient were observed before the treatments and 2 weeks, 1 month, 2 months, 3 months, months,9 months and 12 months after the treatments.All the 37 patients were observed for 12 months. 24 h urinary protein excretion (U-Pro), anti nuclear antibody (ANA), erythrocyte sedimentation rate (ESR), high-sensitivity C-reactive protein (hs-CRP), systemic lupus erythematosus disease activity index (SLEDAI) of these two groups decreased significantly (P < 0.05). serum albumin (ALB), C3, and C4 of two groups were higher after the treatments (P < 0.05). ALB and C3 in treatment group exceeded the control group (P < 0.05). The positive rates of Anti-dsDNA in control and treatment group were 40% and 10% respectively, while the recurrence rates were 50% and 20% respectively, these difference between the two groups were statistically significant (P < 0.05). There were no transplantation related complications observed.UC-MSCs transplantation could be effective and safe for refractory SLE on basis of glucocorticoid and cyclophosphamide therapy.