Background To investigate the retinal and choroidal microvasculature in patients with systemic sclerosis (SSc) who have no clinical evidence of retinopathy and to compare these structures with those of healthy control subjects. Methods Forty-five patients with a confirmed diagnosis of SSc and no clinical evidence of retinopathy and 45 age- and sex-matched healthy control subjects were included in the study. After complete ophthalmological examination, all patients underwent optical coherence tomography angiography (OCTA) measurement (Optovue Inc., Fremont, California, USA) to assess the foveal avascular zone (FAZ) area; FAZ perimeter; acircularity index of FAZ; foveal density-300; superficial and deep capillary plexus vessel densities; and choriocapillaris flow area at 1, 2, and 3 mm radius. The data from the right eyes of all participants were used for statistical analysis. Results The superficial capillary plexus vessel density of the whole image, fovea, parafovea and perifovea, and the deep capillary plexus vessel density of the fovea were significantly lower than those in healthy control subjects (p < 0.05 for all). No significant difference was found in the FAZ area, FAZ perimeter, acircularity index of FAZ, foveal density-300 and choriocapillaris flow area measurements between patients and controls (p > 0.05 for all). Conclusions We demonstrated the ability of OCTA to reveal early retinal microvascular alterations in patients with SSc without any clinical evidence of retinopathy. Reduced vessel density in SSc patients supports the hypothesis of widespread vascular injury, including ocular microcirculation.