Iodine is an important trace element involved in thyroid hormone biosynthesis, while diet-induced obesity is reported to disturb the trace element metabolic balance. Herein, we studied the host-specific responses involved in modulating thyroid function and gut microbiota in obese mice after the iodine treatment and analyzed the possible causes for these responses. Obesity in the mice was induced by a high-fat diet, and the obese and normal mice were treated with the same iodine dosage (18 μg/kg/day) continuously for 8 weeks. Iodine treatment in the obese mice showed a weight-reducing effect, increased the thyroid hormone concentrations, altered the transcriptions of genes involved in thyroid hormone biosynthesis, and modulated the gut microbiota with an increased abundance of pathogenic bacteria and decreased the proportion of beneficial bacteria. However, completely different or even opposite response profiles were observed in the normal hosts. Our work indicated that obesity may exacerbate the risk of thyroid disease with a relatively safe dose of iodine, and individual differences should be considered with trace element supplementation.