The aim of this study was to assess the population's iodine nutrition and thyroid diseases in different water iodine areas and to offer suggestions to the governments of different countries to adjust the present policy in different water iodine areas. A cross-sectional survey was conducted in different water iodine areas in China. Urinary iodine, water iodine, salt iodine and thyroid function were determined. The thyroid volumes and nodules were measured by ultrasound. Upon categorization by water iodine level for the 10.0 ~ 39.9 μg/L, 40.0 ~ 100.0 μg/L and 100.1 ~ 150.0 μg/L areas, in adults, the prevalence of subclinical hypothyroidism was 9.28%, 5.35% and 11.07%, and the median urinary iodine (MUI) was 153.7 μg/L, 189.8 μg/L and 317.0 μg/L; in children of the three areas, the prevalence of goitre was 3.83%, 4.47% and 16.02%, and the MUI was 164.1 μg/L, 221.0 μg/L and 323.3 μg/L; in pregnant women of those areas, the MUI was 148.6 μg/L, 176.9 μg/L and 324.9 μg/L. Logistic regression results indicated that low iodine intake was a risk factor for developing hypothyroxinaemia in pregnant women. The iodine status of pregnant women is insufficient in areas with a median water iodine level of 10.0 ~ 39.9 μg/L. Low iodine intake increases the risk of developing hypothyroxinaemia in pregnant women. The iodine status of adults and children is excessive, and the iodine status of pregnant women is above the requirements in areas with a median water iodine concentration of 100.1 ~ 150.0 μg/L. Iodized salt, especially for pregnant women, should be supplied in areas with a median water iodine concentration of 10.0 ~ 39.9 μg/L to improve the iodine status of pregnant women. Supplying non-iodized salt is not enough to protect local residents from the harm from excess iodine in areas with a median water iodine concentration above 100.0 μg/L.