ABSTRACT Background and objectives Glomerular C3 deposition is often observed in renal biopsies of patients with IgA nephropathy (IgAN), however, the relationship between the level of C3 deposition and the long-term prognosis of IgAN have rarely been reported. In this observational cohort study, we aimed to evaluate the prognostic value of glomerular C3 deposition in the progression of IgAN. Materials and Methods From June 2009 to June 2010, a total of 136 adult patients with IgAN were enrolled in the study. Glomerular deposition of the complement protein C3, immune complexes, and inflammatory cells were detected in renal biopsy tissue. The level of renal lesions, glomerular immune complexes, and the density of interstitial inflammatory cells were analyzed. Based on an average of 105 months of follow-up, the predictive value of glomerular C3 deposition for IgAN progression was investigated. Results Of the 136 patients, 102 patients were classified into the glomerular C3low group and 34 patients were classified into the glomerular C3high group. Patients in C3high group had more immune complexes deposition than those in C3low group. In C3high group, the degree of renal lesion and interstitial fibrosis were severer compared to C3low group. Renal biopsy in C3high group presented with higher density of interstitial inflammatory cells that in C3low group. The density of glomerular C3 deposition was associated with poor renal survival over a 105-month follow-up. Conclusions The high density of glomerular C3 deposition was associated with severity of renal lesions and predicted a long-term poor renal survival for IgAN patients.