Conbercept is a recombinant fusion protein with high affinity for all vascular endothelial growth factor isoforms and placental growth factor. The repeated intravitreal injection of conbercept may cause intraocular pressure (IOP) fluctuations and long-term suppression of neurotrophic cytokines, which could lead to retinal nerve fiber layer (RNFL) damage. This retrospective fellow-eye controlled study included 98 eyes of 49 patients. The changes in IOP and RNFL thickness as well as the correlation between RNFL changes and associated factors were evaluated. The IOP value between the baseline and the last follow-up visit in the injection group and the IOP value of the last follow-up visit between the injection and non-injection groups were not significantly different (p = 0.452 and 0.476, respectively). The global average thickness of the RNFL (μm) in the injection group decreased from 108.9 to 106.1; however, the change was not statistically significant (p = 0.118). No significant difference in the average RNFL thickness was observed at the last follow-up visit between the injection and non-injection groups (p = 0.821). The type of disease was the only factor associated with RNFL thickness changes. In conclusion, repeated intravitreal injections with 0.05 mL conbercept revealed an excellent safety profile for RNFL thickness, although short-term IOP changes were observed.