Familial hypercholesterolemia (FH) is a common but underdiagnosed genetic disorder affecting cholesterol metabolism, leading to atherosclerotic disease. The relationship between retinal microvascular changes and the presence of atheroma in patients with FH (FH group), and in comparison to volunteers without FH (CT group), needs further investigation. This cross-sectional study was conducted in a university hospital between October 1, 2020 and May 31, 2021. Cardiovascular data, including the Coronary Artery Calcium (CAC) score, were recorded for FH patients. Macula angiograms were acquired using swept-source optical coherence tomography angiography (SS OCT-A) to analyze both the superficial capillary plexus (SCP) and deep capillary plexus (DCP). A total of 162 eyes of 83 patients were enrolled in the FH group and 121 eyes of 78 volunteers in the CT group. A statistically significant association was found between the CAC score and both vessel density (β = −0.002 [95% CI, −0.004; −0.0005], p = 0.010) and vessel length (β = −0.00005 [95% CI, −0.00008; −0.00001], p = 0.010) in the DCP. The FH group had a significantly lower foveal avascular zone circularity index than the CT group in multivariate analysis (0.67 ± 0.16 in the FH group vs. 0.72 ± 0.10 in the CT group, β = 0.04 [95% CI, 0.002; 0.07], p = 0.037). Retinal microvascularization is altered in FH and retinal vascular densities are modified according to the CAC score.