Background: Thyroid autoimmunity (TAI), marked by thyroid peroxidase antibodies (TPOAb) and thyroglobulin antibodies (TgAb), affects over 10% of the general population, with children and adolescents experiencing significant impacts on growth and quality of life despite lower prevalence rates compared to adults. Methods: In the context of over 20 years of universal salt iodization (USI) in China, this study investigated the relationship between iodine nutritional status and TAI in children and adolescents aged 6–17. Results: Our findings suggest that while iodine levels are generally sufficient (median urinary iodine concentration [UIC] was 205.2 µg/L), TAI remains a significant concern due to its potential impact on growth and development. TAI was significantly associated with age, sex, and urban–rural residency (p < 0.05). Positive TPOAb and TgAb were identified as risk factors for subclinical hypothyroidism (OR = 2.274, 95% CI: 1.171–1.916). Although some literature suggests that excessive iodine may exacerbate TAI and others propose iodine deficiency as a risk factor, this study did not find a significant overall association between iodine status and TAI. Notably, a low urinary iodine-to-creatinine ratio (UI/Cr) level was linked to an increased risk of TgAb positivity in males (OR = 3.470, 95% CI: 1.200–10.036). In individuals with negative thyroid antibodies, increased BMI (OR = 1.062, 95% CI: 1.032–1.093) and high UI/Cr levels (OR = 1.510, 95% CI: 1.175–1.941) were risk factors for subclinical hypothyroidism, whereas older age (OR = 0.710, 95% CI: 0.555–0.908 for the age 9–11 group; OR = 0.681, 95% CI = 0.484–0.959 for the age 12–17 group) and high UIC levels (OR = 0.739, 95% CI: 0.554–0.985) were associated with reduced risk. No significant associations were observed in the thyroid antibody-positive group. Conclusions: These results highlight the importance of considering individual TAI status when devising iodine supplementation policies.