Aim To investigate the effect of subclinical hypothyroidism in elderly on metabolic syndrome and intracranial atherosclerosis. Methods Randomly selected 416 cases of patients hospitalized in our department from January 2013 to April 2014, including normal thyroid function 298 cases and subclinical hypothyroidism 118 cases. Compared the biochemical indicators of metabolic syndrome, uric acid （UA） and homocysteine （Hcy） in the two groups. Logistic analysis was used to test correlation regarding the intracranial atherosclerosis and metabolic syndrome as dependent variables, and analyze the correlation between thyroid stimulating hormone （TSH） and various clinical indicators. Results Compared with normal thyroid function group, proportions of intracranial atherosclerosis and metabolic syndrome in subclinical hypothyroidism group were obviously increased （P<0.05 or P<0.01）, systolic blood pressure （SBP）, total cholesterol （TC）, triglyceride （TG）, low density lipoprotein cholesterol （LDLC）, uric acid （UA） and homocysteine （Hcy） in subclinical hypothyroidism group were significantly increased （P<0.05）, and high density lipoprotein cholesterol （HDLC）, fasting blood glucose （FBG） were significantly reduced （P<0.05）. Multivariate stepwise Logistic regression analysis found that high levels of TSH, metabolic syndrome, age, SBP, LDLC, Hcy were independent risk factors of intracranial atherosclerosis （P<0.05）, TSH and UA were independent risk factors of metabolic syndrome （P<0.05）. TSH were positively correlated with TG, UA and Hcy, and negatively correlated with HDLC （P<0.05）. Conclusions The occurrence and development of MS and intracranial atherosclerosis was obviously related to high TSH, it may involve in the development of MS, and increases the risk of the crowd intracranial atherosclerosis occurred furtherly.