Objective The objective of this paper is to assess the role of gender on survival rate and causes of death and organ damage in systemic lupus erythematosus (SLE) patients in China from 2009 to 2015. Methods We conducted a multicenter cohort study to analyze the differences in outcome data between male and female SLE patients. A group of 1494 SLE patients who fulfilled the 1997 American College of Rheumatology SLE classification criteria were enrolled in the Chinese Systemic Lupus Erythematosus Treatment and Research Group (CSTAR) registry from April 2009 to February 2010. All enrolled patients were followed up at least once per year from 2009 to 2015. For patients who could not attend the outpatient clinic, follow-up was conducted by telephone interview. We collected demographic data, clinical manifestations and damage scores (System Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SDI)). Survival rates were evaluated using the Kaplan-Meier method. Results This study included 1352 women and 142 men. The five-year survival rates were 92.0% for men and 97.6% for women. The survival rates of males were significant lower than for females (p = 0.019). Male patients received methylprednisolone pulse therapy and cyclophosphamide significantly more than female patients (p = 0.010). During follow-up, 12 male patients and 66 female patients died. The most common cause of death was infection (41.7%) for men and active SLE disease (27.3%) for women. At the end of the study, the major accumulated organ damages included renal (8.5%) and musculoskeletal (7.7%), and nervous system (5.6%) for men and renal (8.8%) and musculoskeletal (6.7%) for women. There were no significant differences in SDI scores between the two groups at baseline and at the end of the study. Conclusions Male SLE patients had lower survival rates than female patients. Male patients received more methylprednisolone pulse and cyclophosphamide therapy. The most common causes of death were infection for male patients and active SLE disease for female patients. The major accumulated organ damages were renal, musculoskeletal, and nervous system both for male and female SLE patients in China.