The aim of the present study was to illustrate the combined effect of excess iodine and low-protein diet on the thyroid, and the potential molecular mechanism of this effect. One hundred ninety-two Wistar rats were randomly divided into the following groups: normal; 10- (10HI), 50- (50HI), or 100-fold excess iodine (100HI); low-protein; and low-protein combined with 10- (L10HI), 50- (L50HI), or 100-fold excess iodine (L100HI). At the end of 2, 4, or 6 months, the rats were sacrificed for iodine concentration and thyroid hormone analyses. The histological appearance of the thyroid gland was observed at the end of 6 months. At the end of 6 months, the serum total thyroxine (TT4), free thyroxine (FT4), total triiodothyronine (TT3), and free triiodothyronine (FT3) levels in the 100HI, L10HI, L50HI, and L100HI groups were significantly lower than the control group (P < 0.05 or P < 0.01). Serum TT4, FT4, TT3, and FT3 levels in the low-protein excess iodine groups were significantly lower than the groups with an equal amount of excess iodine alone (P < 0.05 or P < 0.01). Light and electron microscopy showed that excess iodine caused damage to the ultrastructure of thyroid and apoptosis of follicular epithelial cells. In the 100HI, L50HI, and L100HI groups, thyroid follicular epithelial cells became flattened, and follicles became distended with colloid. The damage was more serious in low-protein groups. The present findings demonstrated that the low-protein diet aggravated the damage to the thyroid caused by excess iodine alone.