Background To evaluate the effects of intravitreal silicone oil (SO) on the retinal and choroidal thickness in eyes with rhegmatogenous retinal detachment (RRD). Methods A literature search was performed in Web of Science, Scopus, ProQuest, Embase, Clinical Key, Science Direct, Cochrane Library, and Springer, as well as Persian databases, including IranDoc, MagIran, SID, MOH thesis, and MOH articles until June 2020. Two reviewers independently searched and extracted the data. Results Sixteen studies (n = 391) met the inclusion criteria. The meta-analysis showed that the SO tamponade could significantly reduce the central macular thickness (CMT) in patients with RRD as compared to gas tamponade WMD = − 14.91; 95% CI: − 22.23, − 7.60; P < 0.001, I2 = 71%). No significant change was found in CMT between the eye with SO tamponade (after SO removal) and the fellow healthy eye in patients with RRD (WMD = − 3.52; 95% CI: − 17.63, 10.59; I2 = 68.6%). Compared to the preoperative stage, the SO tamponade could significantly reduce the subfoveal choroidal thickness in patients with RRD (WMD = − 18.67, 95% CI: − 30.07, − 1.28; I2 = 80.1%). However, there was no significant difference in the subfoveal choroidal thickness before and after SO removal (WMD = − 1.13, 95% CI: − 5.97, 3.71; I2 = 87.6%). Conclusion The SO tamponade had a significant effect on the reduction of retinal layers and the subfoveal choroidal thickness.