To offer a clue for the etiology of amblyopia by systematically comparing the macular thickness measured by optical coherence tomography (OCT) between the amblyopic eye and the fellow normal eye in patients with unilateral amblyopia. Databases including Wanfang, PubMed and others were searched, and data were extracted after quality assessment, then the Meta analysis was performed by the RevMan 5.02 software. Four studies using the time-domain OCT (TD-OCT) were enrolled in the analysis and all those were anisometropic amblyopic patients. The only one study showed that the foveal minimum thickness is thicker in the amblyopic eyes than the fellow ones (P = 0.045). The meta analysis indicated the amblyopic eyes were 6.82 µm (P < 0.05, 95% CI: 2.81-10.83) thicker in the fovea (1 mm diameter region ). Five trials using the spectral-domain OCT (SD-OCT) were included in the analysis. It showed no significant difference in the foveal minimum thickness between amblyopic and fellow eyes. Also, no significant difference were detected in either anisometropic or strabismic subgroup (P = 0.50). Amblyopic eyes were 7.38 µm thicker in the fovea (1 mm diameter region) (P < 0.05, 95% CI: 3.13 -11.63) and significant difference in the anisometropic subgroup while no significant difference in the strabismic subgroup were detected. The macular fovea is thicker in the amblyopic eyes than the fellow ones by the use of OCT, so it is effective to measure the macular thickness of amblyopia in searching evidence for the etiology of amblyopia.