Summary Previous studies have identified an association between iron deficiency and thyroid function. We aimed to determine if there is a relationship between iron deficiency and thyroid function during the first trimester of pregnancy. Two thousand five hundred eighty-one pregnant women who presented for the first prenatal care were enrolled and divided into three groups, the mild iron deficiency (MID) group, iron deficiency anemia (IDA) group and normal control (NC) group, according to serum ferritin and hemoglobin levels. The former two groups can be merged into one iron deficiency (ID) group. Thyroid function parameters were compared among the three groups, including free thyroxine (FT4), thyroid stimulating hormone (TSH), total thyroxine (TT4) and thyroid peroxidase antibodies (TPOAb). Moreover, the rates of thyroid dysfunction were also compared. Our results show that pregnant women in the MID and IDA groups have higher TSH and lower FT4 status than those in the NC group (p,0.01), and the difference between the IDA group and MID group is significant (p,0.05). TPOAb in the IDA group is higher than in the MID group and NC group. Meanwhile, the rate of hypothyroidism or subclinical hypothyroidism in the IDA group was significantly higher than in the MID group and NC group (p,0.01). And the positive rate of TPOAb is also higher in the IDA group than MID group and NC group (p,0.05). Iron deficiency is related to thyroid function and could lead to hypothyroidism during early pregnancy, which could be explained by thyroid autoimmunity.