Patients diagnosed with breast cancer are likely to be diagnosed with thyroid cancer as a second primary cancer. Similarly, patients with thyroid cancer are likely to develop breast cancer. In this study, we found an association between these two types of cancers in the microbiomes of patients with breast cancer. Blood samples were collected from 96 patients with breast cancer, their bacterial extracellular vesicles were isolated, and their microbiomes were analyzed. After microbiome analysis, researchers performed thyroid function tests, estrogen levels, and thyroid ultrasound results of these patients, and the relationships among these parameters were analyzed. Based on the thyroid ultrasonography results, differences in the microbiome were confirmed in the normal, cyst, nodule, and thyroid lobectomy groups. We investigated the microbiome differences between normal thyroid and thyroid cancer. In particular, the abundance of the genus is related to estrogen levels, which could affect thyroid abnormalities and increase thyroid-stimulating hormone levels. This study explains the causes of thyroid cancer in patients with breast cancer using microbiomes and serological tests for thyroid hormones and estrogen. These can be used as basic data for preventing thyroid cancer in patients with breast cancer.