Objective To investigate the relationship between abnormal bone mineral density (BMD) and subclinical thyroid dysfunction. Methods Thyroid function, biochemical indicators of bone metabolism and BMD were reviewed retrospectively in the subjects who received health checkups from July 1, 2009 to January 31, 2017 in the Health Check-up Department of Peking Union Medical College Hospital. People who had thyroid dysfunction, recognized risk factors for osteoporosis, and medication history were excluded. A cross-sectional analysis of thyroid status and biochemical indicators of bone metabolism was performed by the standard methods. BMD at the lumbar spine and femoral neck was measured using dual energy X-ray absorptiometry. Results A total of 6884 subjects (3726 women and 3158 men) were enrolled in the study, with an average age of (50.74 ± 10.41) years. They were divided into three groups:subclinical hyperthyroid, subclinical hypothyroid, and euthyroidism. The alkaline phosphatase in subclinical hyperthyroid group was higher than that in the euthyroidism group[ (67.95±20.64)U/L vs. (63.88±18.99)U/L]. Calcium and phosphorus in blood were higher in both subclinical hyperthyroid and subclinical hypothyroid groups. The rate of abnormal BMD in male euthyroidism, subclinical hyperthyroid and subclinical hypothyroid groups were 36.10％(1049/2906), 29.27％(12/41) and 27.01％(57/211), respectively. The rate of abnormal BMD showed no difference between subclinical hyperthyroid group and euthyroidism group (P>0.05). The rate of abnormal BMD was lower in subclinical hypothyroid group than in euthyroidism group (χ2=7.0901, P0.05). Conclusion There is no significant difference in the rate of abnormal BMD between subclinical thyroid dysfunction group and euthyroidism group, possibly because abnormal serum biochemical indicators preceded the presence of low BMD. More sensitive methods used to determine the status of bone metabolism await to be developed.