Objective To understand iodine and iron nutritional status of lactating women in Aksu Prefecture of Xinjing Autonomous Region, and to provide proper intervention in control of iodine deficiency disorders (IDD) combined with iron deficiency. Methods Four townships as survey points were selected in Baicheng County of Aksu, where severe iodine deficiency was confirmed, 30 to 40 lactating women were investigated for this study in each townships. Samples of urine and drinking water from their family were collected, and then the iodine concentrations were determined. Whole blood was collected by venipuncture for determinations on serum ferritin (SF), serum iron (SI), total-iron-binding capacity(TIBC), and their thyroid function, including FT3, FT4, TSH. Results Median urinary iodine concentration in 137 lactating women was 134.99 μg/L, however, median urinary iodine in lactating women in Daqiao (99.73 μg/L), Tuokexun(44.17 μg/L) of 4 townships was below 100 μg/L. The proportion of urinary iodine below 50 μg/L was higher than 20% in Chaerqi [21.1% (8/38)], Daqiao [21.4% (6/28)], Tuokexun [47.8% (11/25)]. The medium of iodine concentration in drinking water, that was collected from 78 resident families, was 2.15 μg/L. Lactating women of serum SF, SI, FT4, that lower than the normal value, was accounted for 47.6% (59/124), 16.9%(21/124), 11.8% (15/127)respectively. Lactating women of serum TIBC, TSH, that higher than the normal value, was accounted for 20.2% (25/124),10.2% (13/127). Conclusion There is existence in of the combination severe iodine and iron deficiency in a historical serious IDD endemic area in Aksu Prefecture of Xinjiang Autonomous Region, and iron deficiency may be another important environmental factor for the deterioration of IDD prevalence.