Objective To observe the roles of retinal nerve fiber layer thickness (RNFLT) and the macular ganglion cell complex (mGCCT) in the diagnosis of optic atrophy and the evaluation of visual function by using frequency domain optical coherence tomography (OCT). Methods 26 normal eyes and 68 sick eyes were selected from 50 patients with optic atrophy. Best-corrected visual acuity (BCVA) was measured for all the eyes and visual field for those whose BCVA was ≥ 0.05. Frequency domain OCT was used to measure mGCCT and RNFLT. The study evaluated the main parameters provided by OCT in the diagnoses of optic atrophy and their relativities to the visual function indices, such as BCVA and visual field. Furthermore, the study explored the capability of these parameters to distinguish normal optic nerves from optic atrophy and the effects on BCVA. Results In univariate analysis, mGCCT, general loss of volume(GLV), focal loss of volume(FLV) and RNFLT showed significant correlations with all the evaluation indexes(P<0.05). In multiple analysis these significant correlations were found: average mGCCT and GLV with the diagnosis of optic atrophy, average mGCCT and GLV with BCVA, average mGCCT with visual field mean deviation (MD) and visual field pattern standard deviation (PSD), FLV with visual field MD, and GLV with visual field PSD. Average RNFLT showed no correlations with diagnosis of the optic atrophy, BCVA and visual field (P>0.05). Average mGCCT, superior and inferior average mGCCT, average RNFLT, temporal and superior average RNFLT were accurate to diagnose optic atrophy (0.9<AUC<1.0), while inferior and nasal average RNFLT showed moderate accuracy to the diagnosis (0.7<AUC≤0.9). Among the thickness parameters measured by OCT, average mGCCT was accurate to evaluate BCVA(0.9<AUC<1.0), while the others were moderately accurate (0.7<AUC≤0.9). Conclusion The parameters provided by frequency domain OCT especially mGCCT are important in the diagnosis of optic atrophy and evaluation of visual functions.