Objective To investigate the effect of glomerular C3 deposition on clinical and pathological features and prognosis of primary membranous nephropathy (PMN) in children. Methods The clinical data of children diagnosed with PMN by renal puncture from January 2008 to December 2020 were retrospectively analyzed. According to the intensity of glomerular C3 staining by immunofluorescence of renal pathology, the children were divided into low-intensity group (LI group, C3+) and high-intensity group (HI group, C3++ or +++). The clinicopathological features at baseline and treatment outcomes were compared between the two groups. The influencing factors of PMN progressing to end-stage renal disease (ESRD) were analyzed. Results A total of 213 children were included. There were 92 children in LI group and 121 children in HI group. Compared with the LI group, the HI group was older, the 24h urine protein quantity was higher, the serum albumin and eGFR levels were lower, the proportion of massive proteinuria, IgG immunofluorescence staining intensity +++, and IFTA moderate grade were higher, and the differences were statistically significant (P<0.05). The utilization rate of cyclophosphamide in LI group was higher than that in HI group, and the difference was statistically significant (P<0.05). After 43.0 (13.0-85.0) months of follow-up, 92 patients in the LI group completed the follow-up, and one patient progressed to ESRD. Sixty-eight children had complete response (CR) and partial response (PR), and 24 had no response (NR). After 57.0 (20.0-86.0) months of follow-up, 121 patients in HI group completed the follow-up, and five patients progressed to ESRD. Eighty-six children had CR and PR, and 35 had NR. The log-rank test showed that when baseline eGFR≤90 mL·min^-1·1.73 m^-2, the time of progression to ESRD was shorter, and the difference was statistically significant (P<0.05). Multivariate Cox regression analysis showed that increased eGFR at baseline was an independent protective factor for delaying the progression to ESRD (HR=0.96, 95% CI: 0.929-0.987), while glomerular C3 deposition was not associated with the occurrence of ESRD. Conclusions Extensive glomerular C3 deposition is not a predictor of renal failure in children with PMN.