The aim of this study was to determine the risk of myasthenia gravis (MG) in patients with allergic or autoimmune thyroid disease in a large cohort representing 99% of the population in Taiwan. Data from the Taiwan National Health Insurance Database were used to conduct retrospective analyses. The study comprised 1689 adult patients with MG who were 4-fold frequency matched to those without MG by sex, age, and assigned the same index year. Multivariate logistic regression models were used to calculate the odds ratios and 95% confidence intervals for the association between allergic or autoimmune thyroid disease and MG. An increased subsequent risk of MG was observed in the patients with allergic conjunctivitis (AC), allergic rhinitis, Hashimoto thyroiditis, and Graves disease. The adjusted odds ratios (aORs) were 1.93 (1.71-2.18), 1.26 (1.09-1.45), 2.87 (1.18-6.97), and 3.97 (2.71-5.83), respectively. The aORs increased from 1.63 (1.43-1.85) in a patient with only 1 allergic or autoimmune thyroid disease to 2.09 (1.75-2.49) in a patient with 2 thyroid or allergic diseases to 2.82 (2.19-3.64) in a patient with ≥3 thyroid or allergic diseases. MG was associated with the cumulative effect of concurrent allergic and autoimmune thyroid disease with combined AC and Hashimoto thyroiditis representing the highest risk (aOR = 15.62 [2.88-87.71]). This population-based case-control study demonstrates the association between allergic or autoimmune thyroid disease and the risk of MG. The highest risk of subsequent MG was associated with combined AC and Hashimoto thyroiditis.