The studies on the increasing incidence of thyroid abnormalities are scarce. The aim of this current study was to ascertain the effects of geographical region on thyroid abnormalities under the context of universal salt iodization (USI). We randomly selected 1255 participants residing in inland and 1248 in coast, with the determination of urinary iodine concentration (UIC) and functional and morphological abnormalities of thyroid gland. The median UIC was significantly higher for the inland participants (188.5 μg/L) than the coastal participants (128.5 μg/L; p < 0.001), indicating iodine sufficiency in both populations according to the recommended assessment criteria by the World Health Organization. However, the spectrum of thyroid abnormalities varied between regions, with hypothyroidism prevalent in inland and thyroid nodules in coast. The associations between region and thyroid abnormalities via binary logistic regression models showed that the coastal participants were at a higher risk of total thyroid abnormalities than those from the inland (OR 1.216, 95% CI 1.020-1.449), after the adjustment of ten confounders (demographical characteristics, smoking status, metabolism syndrome, and hyperuricemia). These results indicated that further investigations of the adverse effects of hypothyroidism and thyroid nodules on health burden is urgently needed to sustain USI program.