This study analyzed the differences in effects of a 12-week combination of exercise training program with resistance training and aerobic exercises on the risk factors of metabolic syndrome, carotid wall thickness, and thyroid function, between subclinical hypothyroidism patients and obese groups, in middle-aged women. Subjects consisted of either 20 middle-aged women in the subclinical hypothyroidism (SCH) group or 20 obese (body mass indices [BMI], ≥ 25 kg/m) women without hypothyroidism in the obese (OB) group. The body composition, blood lipid factors, hormones associated with thyroid functions, blood pressure (BP), and carotid intima-media thickness were measured, while physical fitness was ascertained. In the SCH group, waist circumference (WC) and high-density lipoprotein cholesterol values were outside the normal ranges, while WC and systolic BP (SBP) were outside the normal ranges in the OB group. Following the 12-week training program, significantly positive changes occurred in body fat percentage, sit and reach test results, and SBP (p < 0.05) in the SCH group, while in the OB group, significantly positive changes in BMI, WC, sit and reach test results, SBP, and diastolic BP (DBP, p < 0.05) were observed. In addition, both groups showed significant decreases in intima-media thickness of the right carotid bifurcation (p < 0.05). However, in the two groups, the 12-week exercise training program did not have similar significant impact on the hormones related to thyroid functions and blood lipids. Therefore, further research on exercise training that can effectively induce changes in the hormones associated with thyroid functions in patients with subclinical hypothyroidism is necessary.