Introduction: The study aimed to assess the ocular toxicity of hydroxychloroquine (HCQ) by confocal microscopy, multifocal electroretinography (mfERG), and scanning laser polarimetry with variable corneal compensation (GDxVCC) in patients with rheumatoid arthritis (RA). Methods: A cross-sectional, comparative case series study was retrospectively conducted on 61 patients under HCQ treatment for RA without fundoscopic anomalies (group 1), 65 RA patients with no HCQ treatment (group 2), and 27 normal subjects (group 3). A comprehensive ophthalmological examination, including confocal microscopy, mfERG, and GDxVCC, was performed in the three groups. Results: In group 1, the duration of treatment ranged from 19 to 96 months (54.9 ± 15.2 months). The mean cumulative dose of HCQ was 446.1 ± 164.0 g (range 114–864 g). Confocal microscopy revealed hyper-reflective abnormal particles in 45 patients (73.8%) and beaded, tortuous fibers in 34 patients (55.7%) in group 1. No corneal change was observed in the other two groups. The mfERG responses in the 6 concentric rings (R1–R6) among the three groups differed except at R3 (all p < 0.05), and data from R1–R6 were not significantly different between groups 2 and 3. The retinal nerve fiber layer thicknesses were statistically thinner in group 1 than in groups 2 and 3 (all p < 0.05). Conclusions: Early signs of corneal and neural retina structure changes were detected in patients with RA treated with HCQ. Whether these findings should be a mark of drug recession still needs further study and more evidence.