The aims of this study were 1) To evaluate retinal nerve fiber layer (fRNFL) thickness and ganglion cell layer plus inner plexiform layer (GCIPL) thickness at the fovea in eyes affected with traumatic optic neuropathy (TON) compared with contralateral normal eyes, 2) to further evaluate these thicknesses within 3 weeks following trauma (defined as “early TON”), and 3) to investigate the relationship between these retinal layer thicknesses and visual function in TON eyes. Twenty-nine patients with unilateral TON were included. Horizontal and vertical spectral-domain optical coherence tomography (SD-OCT) scans of the fovea were taken in patients with unilateral TON. The main outcome measure was thickness of the entire retina, fRNFL, and GCIPL in eight areas. Thickness of each retinal layer was compared between affected and unaffected eyes. The correlation between the thickness of each retinal layer and visual function parameters, including best corrected visual acuity, color vision, P100 latency, and P100 amplitude in visual evoked potential (VEP), mean deviation (MD) and visual field index (VFI) in Humphrey visual field analysis in TON eyes was analyzed. Thicknesses of the entire retina, fRNFL, and GCIPL in SD-OCT were significantly thinner (3–36%) in all measurement areas of TON eyes compared to those in healthy eyes (all p<0.05). Whereas, only GCIPL in the outer nasal, superior, and inferior areas was significantly thinner (5–10%) in the early TON eyes than that in the control eyes (all p<0.01). A significant correlation was detected between retinal layer thicknesses and visual function parameters including color vision, P100 latency and P100 amplitude in VEP, MD, and VFI (particularly P100 latency, MD, and VFI) (r = -0.70 to 0.84). Among the retinal layers analyzed in this study, GCIPL (particularly in the superior and inferior areas) was most correlated with these five visual function parameters (r = -0.70 to 0.71). Therefore, evaluation of morphological change of each retinal layer using SD-OCT can help in understanding TON pathophysiology and indirectly assessing visual function. Moreover, evaluation of the morphological change of the GCIPL in TON eyes may be useful to assess visual function in patients with early TON.