We compared the retinal vessel density and inner retinal thickness in patients who had one eye with geographic atrophy (GA) and a fellow eye with intermediate age-related macular degeneration (iAMD). The vessel density from the superficial vascular complex (SVC) and deep vascular complex (DVC) through optical coherence tomography angiography and the thickness of the nerve fiber layer, ganglion cell–inner plexiform layer (GCIPL), inner nuclear layer (INL), outer nuclear layer (ONL) on a structural optical coherence tomography thickness map were measured in 28 eyes of 14 GA patients with iAMD in the fellow eye. GA eyes had significantly lower vessel density in the SVC (26.2 ± 3.9% vs. 28.3 ± 4.4%; p = 0.015) and DVC (24.2 ± 2.6% vs. 26.8 ± 1.9%; p = 0.003) than fellow eyes (iAMD). GCIPL and ONL were significantly thinner in GA eyes than in the fellow eyes (p = 0.032 and 0.024 in the foveal areas, p = 0.029 and 0.065 in the parafovea areas, respectively). Twenty-four eyes of 12 patients were followed up for 2 years and seven of the fellow eyes (58.3%) developed GA during the follow-up period and showed reduced vessel density in the SVC (26.4 ± 3.0% vs. 23.8 ± 2.9%; p = 0.087) and DVC (25.8 ± 2.2% vs. 22.4 ± 4.4%; p = 0.047) compared to baseline. Vessel density and GCIPL thickness map measurements are potential GA markers in non-neovascular AMD.