Objective · To analyze and compare the subfoveal choroidal thickness and macular ganglion cell layer (MGCL) thickness in hyperopia anisometropic amblyopic children between the amblyopic eyes and the fellow eyes. Methods · The subfoveal choroidal thickness and the MGCL thickness were measuredenhanced depth imaging spectral-domain optical coherence tomography (EDI-OCT) in 63 hyperopic anisometropic amblyopic children. The value of subfoveal choroidal thickness and the MGCL thickness were compared between the amblyopic eyes and the fellow eyes. The average thickness of the eyes between the different types was compared using the paired t test. Results · Mean subfoveal choroidal thickness was (321.83±12.74) μm and (316.78±18.76) μm respectively in amblyopic and fellow eyes (P0.182). Mean MGCL thickness was (83.78±4.81) μm in amblyopic eyes and (83.26±4.17) μm in the fellow eyes (P0.223). Conclusion · Mean subfoveal choroidal thickness and MGCL thickness were not statistically significant between hyperopic anisometropic amblyopic eyes and normal fellow eyes.