Introduction Many studies have shown that differences were observed between male and female lupus patients. Although systemic lupus erythematosus (SLE) affects mostly females (female:male ratio 9:1), male SLE patients show higher mortality due to kidney and neurological disease. Currently there are limited epidemiological data concerning lupus in the Chinese population. As such, the Chinese SLE Treatment and Research group (CSTAR) developed the first online registry of Chinese lupus patients in 2009, and represents a multicenter observational study that attempts to describe and compile the major clinical characteristics of lupus in Chinese patients. Objective To investigate the effect of gender on the phenotypes of Chinese SLE patients. Patients and methods Data for 2104 SLE patients were prospectively collected and included in the CSTAR registry. Patients fulfilled the 1997 American College of Rheumatology (ACR) SLE classification criteria. We conducted a cross-sectional case-control study to analyze patient clinical and laboratory data at onset and at enrollment. SLE disease activity scores (SLEDAI) were also measured at enrollment. Results This study included 1914 women and 190 men. Males and females showed no differences in mean ages at onset, delay of diagnosis and disease duration. Males presented more frequently with fever ( p = 0.003), while musculoskeletal involvement ( p = 0.001) and cytopenia ( p = 0.017) was more common in females as the initial manifestation at onset of SLE. For manifestations at enrollment, males presented more frequently with fever ( p = 0.005), renal disease ( p = 0.019), vasculitis ( p = 0.032) and neuropsychiatric lupus ( p = 0.007). For cumulative manifestations at enrollment, males presented more frequently with discoid rash ( p < 0.001) and neuropsychiatric lupus ( p = 0.036), while less frequently with arthritis ( p = 0.011). However, the laboratory data showed no significant differences between the two groups at enrollment. Males also had higher SLEDAI scores at enrollment ( p = 0.002). Conclusions Renal disease, vasculitis and neuropsychiatric lupus are more common in male SLE patients with higher SLEDAI scores compared to female SLE patients in China.