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This study aimed to explore the relationship between Bipolar Disorder (BD) and endocrine hormones, as well as the relationship between psychotropics and endocrine hormones. We recruited 55 drug-naïve women patients with BD, 66 long-term medicated women patients with BD, and 53 healthy controls. Serum levels of thyroid hormones, reproductive hormones, and insulin were measured in all participants. Clinical symptoms of depression and mania were measured in all patients with BD. After controlling for confounding factors, drug-naïve patients showed higher levels of free triiodothyronine (FT3), FT3/free thyroxine (FT4), and luteinizing hormone (LH) than controls, and medicated patients showed higher levels of FT3/FT4, thyroid stimulating hormone (TSH), anti-müllerian hormone (AMH), and insulin than drug-naïve patients. In addition, medicated patients showed a higher prevalence of subclinical hypothyroidism (24.24%) than drug-naïve patients (1.82%). In General Linear Model (GLM) analysis, use of lithium was associated with TSH levels (β = 0.22, p = 0.034), and use of antipsychotics was associated with AMH (β = 0.38, p = 0.005) and insulin levels (β = 0.27, p = 0.039). BD itself and its medication treatment are associated with alterations of thyroid and reproductive hormones, suggesting BD may interfere with hormone homeostasis through neuroendocrine mechanisms. Lithium, valproate, and antipsychotics should be prescribed carefully in BD patients with pre-existing hormone abnormalities.