Levothyroxine is a class of thyroid hormone medication mainly used in the clinical treatment of thyroid hormone replacement therapy and thyrotropin suppression therapy. In recent years, studies have found a close correlation between the human gut microbiota and the occurrence and development of thyroid diseases, as well as changes in thyroid hormone levels. Therefore, understanding the impact of levothyroxine on the gut microbiota, as well as the effects of the gut microbiota on the metabolism and absorption of levothyroxine, is of great significance for the treatment of thyroid diseases and the rational use of clinical medication. This article explores the interaction between the gut microbiota and levothyroxine and summarizes the current clinical findings of the gut microbiota in levothyroxine therapy.