Objective To analyze the correlation between retinal nerve fiber layer (RNFL) thickness, choroidal microcirculation and radial peripapillary capillary (RPC) in myopes based on a new quantitative method. Methods A cross-sectional study. From April 2019 to January 2020, 100 eyes with high myopia (HM group) and 82 eyes with low-to-moderate myopia (LMM group) were enrolled in Jiangsu Provincial Hospital. All subjects underwent measurements of best corrected visual acuity (BCVA), intraocular pressure, axial length (AL) and spherical equivalent (SE) before anterior segment examination via slip-lamp biomicroscopy, dilated fundus examination, color and red-free fundus photographs and OCT angiography (OCTA). A 4.5mm × 4.5mm scanning area centered on the optic disc was scanned using a frequency domain OCTA instrument, which was divided into 4 quadrants centered on the optic disc by the software automatically. On the scanning laser ophthalmoscope (SLO) and choroidal vasculature images, one ophthalmologist contoured the peripapillary atrophy-β (PPA-β) zones under the supervision of another veteran ophthalmologist before calculating the area and choroidal vessel density of PPA-β zone using PyCharm software. The correlation between AL, SE, the area and vessel density of PPA-βzone, peripapillary RNFL thickness and RPC vessel density was analyzed by Spearman correlation analysis and multivariate linear regression model. Results The difference in average, nasal, superior and inferior RNFL thickness and RPC vessel density, as well as the area and choroidal vessel density of PPA-β zone was statistically significant between HM and LMM groups (P < 0.05). SE, average peripapillary RNFL thickness and the choroidal vessel density of PPA-β zone were positively correlated with the average blood flow density of RPC (P < 0.001), while AL and the area of PPA-β zone were negatively correlated with RPC vessel density (P < 0.001). The multivariable model revealed that only average RNFL thickness (P < 0.001) and the area of PPA-β zone (P = 0.014) were associated with average RPC vessel density. The results of Spearman correlation analysis for 4 quadrantile subgroups indicated that RNFL thickness remained positively correlated with RPC vessel density (P < 0.001). Conclusion Peripapillary RNFL thickness and the area of PPA-β zone were two crucial causes of RPC vessel density changes, which may indicate the close relationship between retinal constructure and microvascular changes and emphasize the importance of myopia-related optic neuropathy.