The thymus is a central immune organ for T cell development and plays an extremely important role in immune and aging. The unique physiological processes that occur in women, such as the menstrual cycle, pregnancy, and menopause, contribute to sexual dimorphism in thymic immunity. Thymic epithelial cells (TECs) are key stromal cells that affect thymus development and degeneration. Interestingly, TECs in women have stronger proliferation potentiality and ability for output of T cells than those in men. In comparison to men, women exhibit higher susceptibility to autoimmune disease, which can be attributed to lower AIRE expression in the female thymus, which is influenced by fluctuating hormone levels. In this review, we summarize the principles of female thymus regulation by hormones, particularly the influence of female sex hormones in the development and function of TECs, as well as the underlying mechanisms, with the aim of providing new ideas and strategies to inhibit or slow down female thymus degeneration.