The detection of hormone levels plays an important role in the diagnosis and treatment of endocrine diseases. Mass spectrometry, a very valuable tool in the field of hormone detection, can provide more accurate and comprehensive information for the diagnosis of disease because of its high specificity, high sensitivity and the ability to detect multiple compounds at one time. It plays a key role in improving or changing the clinical diagnosis, treatment and management of some endocrine diseases. But now the application of mass spectrometry in endocrine hormone is not common in China, and the comprehensive report is rare. This article will focus on the current mass spectrometry in the diagnosis and treatment of endocrine diseases with prominent advantages and applications of more mature areas including adrenal diseases in pheochromocytoma and paraganglioma, Cushing′s syndrome, primary aldosteronism and congenital adrenal cortical hyperplasia, thyroid disease in thyroid function assessment and detection of androgens and estrogens in glandular disease. We will detailed demonstrate the application of mass spectrometry in the field of these diseases. The advantages and challenges of mass spectrometry in the endocrine diseases are analyzed. The trend and direction of mass spectrometry in the diagnosis and treatment of endocrine diseases are prospected.