Objective To evaluate the incidence of autoimmune thyroid diseases in naval soldiers under different environments, so as to take early prevention and control measures. Methods The data of 2 198 naval officers and soldiers who underwent physical examination in the Physical Examination Center, The First Affiliated Hospital of Naval Medical University (Second Military Medical University) from Jun. to Sep. 2020 were retrospectively analyzed. The officers and soldiers were divided into urban groups (stationed in coastal cities) and ship groups (stationed in ships) according to their stations. The levels of serum triiodothyronine (T₃), thyroxine (T₄), thyroid-stimulating hormone (TSH), thyroid peroxidase antibody (TPOAb) and thyroglobulin antibody (TgAb) and thyroid ultrasound results were compared. Multivariate logistic regression was used to analyze the influencing factors of thyroid function, thyroid antibody level and thyroid ultrasound results. Results There were 1 095 cases in the urban group, with a median age of 34 (29, 41) years, including 663 males (60.55%) and 432 females (39.45%), and 1 103 cases in the ship group, with a median age of 33 (28, 38) years, including 1 014 males (91.93%) and 89 females (8.07%). There were significant differences in gender and age between the 2 groups (P<0.01). In the urban group, there were 111 cases (10.14%, 111/1 095) of abnormal thyroid antibodies, 9 cases (0.82%, 9/1 095) of subclinical hyperthyroidism, 85 cases (7.76%, 85/1 095) of subclinical hypothyroidism and 363 cases (45.72%, 363/794) of thyroid nodules. In the ship group, there were 84 cases (7.62%, 84/1 103) of abnormal thyroid antibodies, 5 cases (0.45%, 5/1 103) of subclinical hyperthyroidism, 38 cases (3.45%, 38/1 103) of subclinical hypothyroidism and 258 cases (33.64%, 258/767) of thyroid nodules. Multivariate logistic regression analysis showed that the gender was correlated with abnormal thyroid antibody level (P<0.01), station and thyroid antibody level were the influencing factors of TSH (both P<0.01), and gender, age and thyroid antibody level were related to the incidence of thyroid nodules (all P<0.01). Conclusion The naval officers and soldiers stationed in coastal cities have higher incidence of abnormal thyroid antibody, subclinical hypothyroidism and thyroid nodules. For female naval officers and soldiers, prevention and control measures should be taken earlier, and the benign or malignant of the nodules in female naval officers and soldiers with elevated thyroid antibodies need to be further evaluated with the increase of age.