Macro thyroid-stimulating hormone (TSH) has been reported to be associated with seasonality and regulated by changes in day length in rodents, different from free TSH. In the present study, we investigated structural differences between macro TSH and free TSH levels in human serum, as well as the association of macro TSH with sleep quality. We enrolled 314 patients registered in the Hyogo Sleep Cardio-Autonomic Atherosclerosis (HSCAA) study. Sleep quality shown by actigraphy, sleep physical activity, and percent sleep in all and TSH closely matched subjects were significantly associated with high macro TSH levels. Macro and free TSH were similarly increased following thyrotropin-releasing hormone (TRH) stimulation, while circadian changes associated with those were distinct. To further analyze the structure of macro TSH, serum samples were separated by gel filtration chromatography. Although treatment with glycosidase did not affect morbidity, the macro TSH fraction had a markedly low affinity to the Con A column as compared with free TSH, indicating a distinct glycosylation structure. In conclusion, an increase in serum macro TSH is associated with low sleep quality and regulated in a manner distinct from free TSH, potentially due to an altered glycosylation structure.