To compare and assess the choroidal and retinal microstructural vascularity in amblyopic eyes with the fellow eyes in anisometropic amblyopic children using angiography optical coherence tomography (Angio-OCT). Twenty-seven children (54 eyes; 5.59 ± 1.08 years old; 59.3% girls) were enrolled in this study. Choroidal thickness (CT) was measured with the use of the enhanced depth imaging mode in Angio-OCT. Parafoveal/peripapillary vascular density indices and the foveal avascular zone (FAZ) size were analyzed by MATLAB code programming on Angio-OCT images. The mean FAZ size of the amblyopic eyes were larger both in superficial and deep capillary plexus layer (SCPL/DCPL). Compared with the contralateral eyes (BCVA were normal), all the vascular density indices of SCPL and DCPL in the parafoveal and peripapillary zones were lower in the amblyopic eyes, however, the difference was insignificant (p > 0.05). No significant decrease was observed in four quadrants analyses of the amblyopic eyes (p > 0.05). Except for the measurement at 2000 µm and 1500 µm from the fovea in temple, CT in amblyopic eyes were significantly thicken than the fellow eyes (p < 0.05). Compared with the fellow eyes, the CT of certain areas were thicker in the amblyopic eyes. Though the FAZ size of the amblyopic eyes was larger in SCPL/DCPL layers, the retinal vascular density indices in SCPL/DCPL were lower in amblyopia eyes without statistical difference. Angio-OCT may be an effective way to evaluate the status of the choroidal and retinal vascular system in amblyopic children.