Objective：The objective of the study was to investigate the association between thyroid stimulating hormone（TSH） and incident non-alcoholic fatty liver disease（NAFLD） in middle-aged and elderly population in a 3-year follow-up study. Methods：Total 222 subclinically hypothyroid（TSH>4.50 mU/L）and 727 euthyroid people aged 40~75 years who were free of fatty liver disease at baseline in a community were included in the current study. The study population was screened initially in 2011 and re-evaluated in 2014. On both occasions they were assessed by structured interview via a questionnaire on general information，anthropometric measurements，thyroid hormones，biochemical and serological tests，liver ultrasound. Results：Among 222 baseline subclinical hypothyroidism patients，62（27.93%） reverted to euthyroidism at a 3-year follow-up. The 3-year incidence of subclinical hypothyroidism was 16.64%（121/727）. Higher TSH levels at baseline were associated with higher total cholesterol（TC），triglyceride（TG），low density lipoprotein cholesterol（LDL-C） and aspartate aminotransferase（AST） levels（P < 0.05）. The incidence rate of NAFLD increased with increasing baseline TSH levels in female（P < 0.05）. Logistic regression analyses showed，higher baseline TSH levels were associated with the diagnosis of NAFLD by unadjusted in model 1 in female. After adjustment for age，baseline BMI，baseline TG，baseline HbA1c in model 2，this association remained significant. When data were adjusted for the changes in BMI and changes in HbA1c in model 3，the association was no longer significant. Conclusion：Among middle-aged and elderly population，baseline TSH was an influencing factor，but not an independent risk factors，for 3-year incidence of NAFLD in female.