Background: Obesity is more easier exhibiting subclinical hypothyroidism (SH) and acanthosis nigricans (AN). We aimed to elucidate the thyroid hormone levels in obese patients and its association with fat distribution and AN. Methods: In this cross-sectional study, 202 obese men and 239 obese women were enrolled. Anthropometric measurements, glucose-lipid metabolism, thyroid hormone levels and fat distribution were measured. SH were defined by thyroid stimulating hormone (TSH) less than 2.5 mU/L. Results: 1) The prevalence of AN was significantly higher in obese group with SH than without SH (47.3% vs. 36.9%, P=0.035). Number of obese women with SH were larger than men (38.1% vs. 28.2%, P=0.029). Obese women have higher TSH levels, lower free triiodothyronine (FT3) and free thyroxin (FT4) than obese men (all P<0.01). Body mass index (BMI), waist/hip ratio (WHR), glycosylated hemoglobin (HGB), homeostasis model of assessment for insulin resistance index (HOMA-IR) were significantly lower in obese women than men (all P <0.05). 2) In all obesity, FT3 was significantly positively associated with height, weight, NC, WC, WHR, SBP, DBP, FINS, UA and negatively with HDL-C (all P <0.05). FT4 was significantly positively associated with height, weight, BMI, NC, WC, SBP, DBP, UA, HGB and FBG (all P <0.05). TSH was negatively with FBG and HGB (all P <0.05). 3) FT3 was positively with Peripheral fatmass, total leanmass and negatively with Total Fat% and Trunk/peripheral fatmass (P=0.025;P=0.029;P<0.001;P=0.034), FT4 was also positively with total leanmass and negatively with Total Fat%(P=0.008; P=0.017), and TSH was positively with Total Fat%(P=0.032). Conclusion: AN is more likely to happen in the obesity with SH. Obese women have higher probability of SH than men. Relatively slightly insufficient of thyroid function with higher TSH may be protective factor in obese women with better metabolism. Thyroid hormone may beneficial to improving fat distribution and building lean mass in the obesity.