Background The study aims to evaluate peripapillary retinal nerve fiber layer thickness (RNFL-T), central macular thickness (MT), choroidal thickness (CT), and thickness of each retinal layer after automatic segmentation in patients who underwent retinal detachment (RD) repair with longstanding silicone oil tamponade. Methods We enrolled 33 patients who underwent complicated primary rhegmatogenous RD surgery and followed up with a long-term silicone tamponade were included in this retrospective comparative (case-control) study. RNFL-T, CT, and thickness of each retinal layer after automatic segmentation analysis were measured after the longstanding silicone removal surgery. Results The mean silicone oil removal time was 15.1 +/- 15.2 (7-70) months. The overall average thickness of the RNFL was 90.7 +/- 13.6 mu m in the operated eyes and 118.3 +/- 35.6 mu m in the sound eyes, with a statistically significant difference. The overall average central MT was 186.3 +/- 57.7 mu m and was significantly lower in the operated eyes than in the sound eyes. Inner retinal layers of the study group showed a significant thinning in the nerve fiber layer, ganglion cell layer, inner plexiform layer, and inner nuclear layer as compared to that of the sound eyes. The subfoveal CT was 213.7 +/- 86.6 mu m in the study eyes and 217.7 +/- 115.5 mu m in the control eyes. There was no significant difference between the study eyes and controls. Conclusion The effects of silicone oil on the retina remain uncertain; however, morphological results in our study have shown direct or indirect silicone oil-induced toxicity, especially in the inner retinal layers.