To investigate the changes in axial length and retinal thickness and their relationships with myopia in highly myopic anisometropia. A total of 87 Chinese subjects (25.28±11.98 years, mean±SD) were divided into two groups: anisometropia (n=38) and nonanisometropia (n=49). All eyes were measured for axial length, refractive status, and macular thickness (optical coherence tomography). Ocular biometric results were compared between eyes of subgroups. Linear correlation between refractive error and other biometric results was performed. In the anisometropic group, the inner ring macula and part of the outer ring macula (nasal and inferior quadrants) in the higher myopic eyes were significantly thinner than in the fellow eyes (P≤0.007), but the foveal thickness (minimum and average) was similar (P≥0.050) between the two eyes. However, the minimum and average foveal thicknesses were found to be significantly thicker in the highly myopic eyes than those in the emmetropic to moderate myopic eyes (P≤0.016) in the nonanisometropic group. Among the eyes ranging from emmetropia to high myopia, the refractive error was negatively correlated to the axial length of the eye (P<0.001) and the thinning of inner ring macula is consistent with the increase in both myopia and axial length. There was a negative correlation in refractive error and axial length but no correlation in parafoveal thickness between eyes of the same subjects (P<0.001) in the anisometropic group. In people with myopic anisometropia, the higher myopic eye has a longer axial length but a thinner parafoveal region than its fellow eye. The axial growth in the development of high myopia seems to be centrally regulated; however, the changes in parafoveal thickness are likely manipulated by local mechanisms within the eye.