The pathogenesis of maculopathy remains incompletely understood, and emerging evidence implicates the gut–eye axis in retinal and macular diseases. Given that antibiotics with anti-anaerobic activity may disrupt gut microbial ecology, this study investigated their association with the risk of incident maculopathy. We conducted a nationwide population-based study using the National Health Insurance Service–National Sample Cohort of South Korea. A retrospective cohort study was used to assess cumulative systemic anaerobic antibiotic exposure during a 5-year baseline period and subsequent incident maculopathy from 2007 to 2019. After 1:1 propensity score matching, hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression. A nested case-control study was also conducted using risk-set sampling and 1:10 propensity score matching. Anaerobic antibiotic exposure during the 365 days before the index date was assessed, and odds ratios (ORs) and 95% CIs were estimated using conditional logistic regression. Duration-response relationships were evaluated using formal trend analyses. Sensitivity analyses included age restriction, Fine-Gray competing risk models, extended exposure assessment windows, lag-time analyses, and a negative control comparator analysis using first-generation cephalosporins. In the retrospective cohort study, 326,436 anaerobic antibiotic users were matched to 326,436 non-users. Anaerobic antibiotic use was associated with an increased risk of incident maculopathy in the fully adjusted model (HR, 1.07; 95% CI, 1.03–1.12), with a significant duration-response trend and the highest risk observed for ≥57 days of cumulative use (HR, 1.24; 95% CI, 1.09–1.42). In the nested case-control study, 55,776 cases were matched to 557,760 controls. Anaerobic antibiotic use within 365 days before the index date was associated with increased odds of maculopathy (OR, 1.04; 95% CI, 1.02–1.07), also showing a significant duration-response trend. Sensitivity analyses and first-generation cephalosporin comparator analyses, generally supported the robustness of the findings. Systemic exposure to antibiotics with anti-anaerobic activity was associated with an increased risk of incident maculopathy, with a duration-response pattern across cumulative exposure categories. These findings suggest further investigation into gut microbiome disruption and the gut-eye axis as potential pathways involved in maculopathy.