Gut microbiota has a close connection to different thyroid disorders, yet research on its links to subclinical hypothyroidism (SCH) remains limited and insufficient. In this study, we explored the potential relationship between the gut microbiota and SCH, as well as dyslipidemia in SCH mice. The SCH mouse model was induced using methimazole. The composition of the gut microbiota from mice was then analyzed through 16S rRNA gene sequencing technology. An antibiotic disruption experiment was used to assess how gut microbiota imbalance impacts thyroid function. The SCH mouse models were constructed and accompanied by significant dyslipidemia. The results revealed no significant differences in the Firmicutes to Bacteroidota ratio or α-diversity in gut microbiota from SCH and control mice, and in β-diversity, there was a noticeable but small difference between the groups. 14 differential genera between the two groups identified through LEfSe analysis were significantly correlated with serum lipid levels. Furthermore, the results of the antibiotic disruption experiment demonstrated that gut microbiota imbalance exacerbated the hypothyroidism in mice. The present results suggest that subclinical hypothyroidism has not yet caused significant changes in gut microbiota homeostasis, but gut microbiota plays an important role in regulating thyroid function and is closely associated with dyslipidemia in SCH. This study could help understand the relationship between gut microbiota and SCH, and offer new perspectives on dyslipidemia management in SCH.