Objective To investigate the relationship between different chromosome karyotypes and the incidence of autoimmune thyroid disease (AITD) and thyroid function in children with Turner syndrome (TS). Methods A total of 93 children with TS diagnosed by chromosome karyotype since 2013 were analyzed. The detailed distribution of AITD and abnormal thyroid function in each group of chromosome karyotypes and the correlation between them were analyzed. Results Of the 93 children with TS, 21 (22.6%) had AITD at initial diagnosis, of whom 17 had normal thyroid function, 1 had subclinical hypothyroidism, 1 had clinical hypothyroidism, and 2 had hyperthyroidism. In addition, 21 children with AITD were regularly reviewed at a median interval of 3 years to evaluate the change of thyroid function status over time. Among them, 10 patients had normal thyroid function, 4 had subclinical hypothyroidism, 3 had clinical hypothyroidism, and 4 had hyperthyroidism. The AITD group was divided into 3 subgroups according to karyotype (8 cases of 45, X chromosome monomer in subgroup A1, 1 case of chimeric type in subgroup A2 and 12 cases of X chromosome structural abnormality in subgroup A3). At the end of follow-up, the incidence of thyroid dysfunction in each group increased significantly over time. Conclusions Thyroid function deteriorates progressively over time in children with Turner syndrome. The older the age at first diagnosis of AITD, the higher the incidence of thyroid deterioration. Patients with Turner syndrome need regular monitoring of thyroid function and prompt treatment.