Exosome, as the critical communication carrier secreted by cells, has been demonstrated to carry non-coding RNA (ncRNA) that participate in regulating the onset and progression of various female reproductive system diseases. In this review, the roles of exosome ncRNA (such as microRNA, long ncRNA, and circular RNA) in non-tumor diseases of the female reproductive system were reviewed, including premature ovarian failure, polycystic ovary syndrome, and endometriosis, as well as in female reproductive system tumor diseases such as ovarian cancer, cervical cancer, and endometrial cancer. The theoretical basis and broad application prospects for the development of non-invasive diagnostic markers, prognostic evaluation tools, and potential therapeutic targets based on exosome ncRNA were provided.