ABSTRACT Clinical relevance The morphological characteristics of the optic nerve head (ONH) in myopic eyes are a clinically significant issue, especially for high myopia in school-aged children, and this can be monitored using optical coherence tomography. Background The purpose of this study is to investigate the morphological characteristics of ONH, and the factors associated with peripapillary choroidal thickness in Chinese school-aged high myopia children. Methods A total of 48 patients, possessing 48 high myopia eyes and 48 contralateral low myopia eyes were enrolled. The ONH characteristic parameters, including peripapillary retinal nerve fibre layer thickness, peripapillary choroidal thickness, peripapillary choroidal blood flow density, Bruch’s membrane opening (BMO) characteristic parameters were measured on optical coherence tomography scans. Results Eyes with high myopia had a larger disc size, higher peripapillary atrophy area proportion, larger peripapillary atrophy area, larger BMO minimum rim width, lower peripapillary choroidal thickness compared with those contralateral low myopia eyes (all P < 0.001). The BMO distance and border length were longer, and border tissue angle was smaller in the high myopia eyes. The multivariate regression analysis revealed that border length, axial length, and border tissue angle were independently associated with peripapillary choroidal thickness (all P < 0.05); axial length was associated with peripapillary retinal nerve fibre layer thickness (P = 0.007). Conclusion The peripapillary atrophy area, BMO area, border length, BMO distance, and BMO minimum rim width increased, but peripapillary choroidal thickness, retinal nerve fibre layer thickness decreased with axial elongation of the globe in young myopia children. Longer axial length and border length were positively correlated with lower peripapillary choroidal thickness, and a smaller border tissue angle was positively correlated with lower peripapillary choroidal thickness were found in this study. Monitoring of border length and border tissue angle is essential in the early stages of myopia in children.