Autoimmune thyroid diseases (ATDs) are potentially connected to lacrimal gland dysfunction and ocular surface disruption. This study aimed to evaluate the relationships between ATD, dry eye disease (DED), and corneal surface damage. In a matched nationwide cohort study, we used Taiwan’s National Health Insurance research database to compare the incidences of DED and corneal surface damage between subjects with and without ATD. Multivariable Cox proportional hazards regression models were used to estimate the adjusted hazard ratio (aHR) and 95% confidence interval (CI) for the ophthalmological outcomes. A total of 50,251 matched pairs with 748,961 person-years of follow-up were included for analysis. The incidence of DED was 16.37 and 8.36 per 1000 person-years in the ATD and non-ATD groups, respectively. ATDs were significantly associated with increased DED (aHR: 1.81, 95% CI: 1.73–1.89,p< 0.0001). This association was generally consistent across the subgroups of age, sex, different comorbidity levels, and use of systemic corticosteroids or not. Furthermore, patients with ATD had a higher risk of corneal surface damage compared with non-ATD subjects (aHR: 1.31, 95% CI: 1.19–1.44,p< 0.0001), including recurrent corneal erosions (aHR: 2.00, 95% CI: 1.66–2.41,p< 0.0001) and corneal scars (aHR: 1.26, 95% CI: 1.01–1.59,p= 0.0432). Other independent factors for corneal surface damage were age, sex, diabetes mellitus, Charlson Comorbidity Index scores, and use of systemic corticosteroids. Our results suggested that ATDs were associated with higher risks of DED and corneal surface damage. Considering the high prevalence of ATD, prophylactic and therapeutic strategies should be further developed to prevent irreversible vision loss in this susceptible population.