Immunophenotypes are related to the therapeutic efficacy of specific immunomodulating agents in patients with myasthenia gravis (MG), but the relationship of immunophenotype to the presence or absence of thyroid antibodies is unknown. This study aims to evaluate differences in the immunophenotypes between MG patients with and without thyroid antibody (TAb) positivity to provide insight for future targeted immunotherapies.This retrospective observational study included 48 MG patients with acetylcholine receptor antibody (AchR-Ab), of which 15 (31.25%) were TAb positive. Ocular MG (OMG) was defined as ocular-only manifestations for the duration for which records were available. Peripheral lymphocyte subpopulations were measured by flow cytometry.TAb positive patients appeared to have a higher prevalence of OMG than TAb negative patients (53.33% vs. 24.24%, p  = .048). Percentages of B cells (mean difference (MD) = 6.16, 95% confidence interval (CI): 1.91-10.40, p = .007) and CD8 + CD28+ cells (MD = 15.14, 95%CI: 5.17-25.11, p  = .013) were higher in TAb positive patients than those in TAb negative patients, while AChR-Ab titers (MD = -6.49 nmol/L, 95%CI: -9.29 to -3.70, p  < .001), percentages of T cells (MD = -6.43, 95%CI: -11.92 to -0.94, p = .023), CD3 + HLA-DR+ cells (MD = -6.47, 95%CI: -12.31 to -0.63, p  = .031) and CD8+ T cells (MD = -6.60, 95%CI: -9.86 to -3.34, p < .001) were lower.The immunophenotypes of MG patients with and without TAb positivity were significantly different, suggesting that their sensitivity to immunotherapy may be different. Further studies focused on differences between TAb positive and TAb negative MG patients in their responses to specific immunotherapies are needed to support our exploratory findings.© 2022 Wiley Periodicals LLC.