Objective Using a hydrogen coupled methane lactulose breath test (LBT) and associated clinical indices, the link between small intestinal bacterial overgrowth (SIBO) and hypothyroidism in early pregnancy. Methods The methane hydrogen breath test included 200 patients with early-stage hypothyroidism, 200 normal pregnant women, 200 normal women of childbearing age prior to pregnancy. Comparisons were made between the incidence, smooth curve fitting, clinical signs, and clinical test results of SIBO. Results The positive rates of SIBO were 62.00%, 28.50%, and 20.50%, respectively, in the hypothyroidism during pregnancy group, the normal pregnant women group, and the normal women group before pregnancy. p < 0.001 indicates that the difference was statistically significant. Additionally, thyrotropin (TSH) and methane hydrogen exhalation volume showed a positive connection in patients with hypothyroidism during pregnancy (p < 0.01, Std = 0.163).In the three groups, the abdominal distension symptoms of patients with SIBO were significantly higher than those of patients without SIBO(p = 0.017,p < 0.001,p < 0.001).Patients with hypothyroidism complicating SIBO had greater levels of TSH, TPOAb, C-reactive protein, and FT4, whereas their levels of vitamin D were decreased(p < 0.001,respectively).Conclusion Intestinal bacterial overgrowth and hypothyroidism during the first trimester and pregnancy are closely associated; the connection between these two conditions may also involve inflammatory agents and vitamin levels.