We investigated the relationship between microstructure of β-parapapillary atrophy (β-PPA) and morphologic features of optic nerve head (ONH) and posterior pole in highly myopic eyes. Eighty-nine highly myopic eyes were included in this study. Bruch's membrane opening (BMO) area, lamina cribrosa (LC) thickness, anterior laminar depth, peripapillary and subfoveal choroidal thickness (CT), macular Bruch's membrane (BM) length, and width of β-PPA with and without Bruch's membrane (PPA+BM and PPA-BM) were evaluated. The mean age and axial length of the included subjects were 26.88 ± 2.44 years and 27.03 ± 0.88 mm, respectively. The width of PPA-BM was larger with increasing BMO area (P = 0.001), whereas the BMO area was not associated with the width of PPA+BM. The large PPA+BM was significantly related to a thinner LC (P = 0.003), deeper anterior lamina surface (P < 0.001), longer macular BM length (P = 0.008), and thinner temporal peripapillary CT (P = 0.034). We found that the morphologic features of the ONH and posterior pole in highly myopic eyes were different based on the microstructure of β-PPA. Whether these features are linked to the development of glaucoma in myopic eyes should be investigated in future studies.