The aim of the study was to evaluate changes in the retinal thickness and microvasculature based on optical coherence tomography (OCT) depending on baseline oxygen saturation (SpO2) in patients hospitalized due to COVID-19 bilateral pneumonia. The prospective study was carried out among 62 patients with COVID-19 pneumonia who underwent ophthalmic examination after hospital discharge. They were divided into three groups depending on the oxygen saturation (SpO2) on admission: ≤90% (group 1), >90% and ≤95% (group 2), and >95% (group 3). The following parameters were assessed in the ophthalmological examination and correlated with the baseline SpO2: ganglion cell layer (GCL), the retinal nerve fiber layer (RNFL) in the macular area, RNFL in the peripapillary area, the foveal avascular zone (FAZ) in superficial capillary plexus (SCP) and deep capillary plexus (DCP), vessel density (VD) in SCP, in DCP, and in the choriocapillaris plexus (CC). Baseline saturation ≤90% in COVID-19 patients caused a decrease of VD in some areas of SCP and DCP and an increase in FAZ area in SCP and DCP. In the group of patients with SpO2 ≤ 90% statistically significant thinning of the retina in the inner superior ring (ISR) (p = 0.029), the inner temporal ring (ITR) (p = 0.34), the outer superior ring (OSR) (p = 0.012), and the outer temporal ring (OTR) (p= 0.004)] was observed. The statistically significant thickening of RNFL optic disc and thinning of RNFL retina in some macular areas in patients with SpO2 ≤ 90% were reported. The size of FAZ area in SCP and vessel density were significantly greater in some areas of SCP, DCP, and CC in patients with SpO2 ≤ 90% (p = 0.025). Baseline oxygen saturation ≤90% has been found to influence the ocular parameters of OCT in COVID-19 patients. We noticed a widened FAZ zone in SCP and increased VD in some regions of the retina and choroid as a response to systemic hypoxia.