To compare large- and medium-sized choroidal vascularity and the choriocapillaris (CC) flow area in children with different refractive errors using swept-source optical coherence tomography angiography (SS-OCTA). Forty-two anisometropic children were enrolled and divided into hyperopic anisometropia (HA) and myopic anisometropia (MA) groups. SS-OCTA was performed to analyse choroidal vascularity. Mean choroidal thickness (CT), choroidal vascularity volume (CVV), choroidal vascularity index (CVI) and CC flow area were compared between the two eyes. The inter-ocular differences between the two groups were also determined. Mean CT and CVV were highest in eyes with shorter axial lengths in both refractive groups, and the difference between the two eyes was positively correlated with the difference in axial length at the foveal region. Significant differences in the CVI in the MA group were only found in the parafoveal region. Inter-ocular differences in the CC were significantly reduced in eyes with longer axial lengths in the foveal and parafoveal regions of the HA and MA groups, respectively. Comparing inter-ocular differences, CC was significantly greater in the parafoveal region of the MA group than the HA group. All layers of choroidal vasculature were thinner in eyes with longer axial lengths in all groups. The inter-ocular CC difference was greater in the MA than in the HA group, with similar differences in axial length. This suggests that both medium-to-large choroidal vascular and choroidal capillaries may play a role in myopia development.