The quality of the scan image is important in peripapillary circulation analysis using optical coherence tomography angiography (OCTA). We aimed to investigate the effects of signal strength (SS) on the peripapillary microvascular density acquired from OCTA. A total of 259 eyes from 259 young healthy subjects were included. Peripapillary OCTA images using 3 × 3 mm angiography scan were acquired from all participants. Subjects were divided into four groups according to the SS: SS 7, SS 8, SS 9, and SS 10. Vessel density (VD) and perfusion density (PD) of the superficial capillary plexus were calculated. VD and PD were compared among the four groups, and linear regression analyses were performed to identify and evaluate the clinical factors associated with average VD. As the SS increased from 7 to 10, the average VD and PD increased; these increases were statistically significant (all, p < 0.001). Regression analyses showed that four factors were significantly correlated with average VD: age (partial r = 0.133), average retinal nerve fiber layer thickness (partial r = 0.169), cup/disc ratio (partial r =-0.481), and SS (partial r = 0.413). SS is a significant factor affecting peripapillary microvascular density, and its influence is similar to well-known structural parameters associated with glaucoma.