Recent genome-wide association scans and replication studies reinforce that FCGR2A is a susceptibility gene in systemic lupus erythematosus (SLE) in Caucasians. However, previous case control studies denied such conclusions in Chinese people. Besides genetic heterogeneity among different ethnicities, copy number variation (CNV), non-homogenous phenotypes and insufficient power may be confounders. We performed a case control study with 1066 Chinese (589 SLE patients and 477 healthy controls) and a meta-analysis based on 2328 SLE patients and 2313 healthy controls. FCGR2A CNV and FCGR2A131H/R [rs1801274] were detected by TaqMan assays. No variation of copy numbers of FCGR2A gene was found in Chinese. A further case control study suggested a dose-response character for FCGR2A131H/R and it affected disease activity, severity and prognosis. Finally, meta-analysis indicated FCGR2A that was a susceptibility gene to SLE in Chinese with an odds ratio of 1.094 and population attributable risk proportion of (PARP) 0.031. By an integrative strategy, we validate that FCGR2A bears no population-specific CNV. FCGR2A131H/R contributes to SLE susceptibility in Chinese, and affects disease activity, severity and prognosis. The undetected association in Chinese derives from under-power rather than any methodological obstacle due to CNV or population-specific genetic effect.