The complex microbiome that resides in the human body plays a crucial physiological role, closely linked to both the maintenance of human health and the onset of diseases. In recent years, microorganisms have been detected in sites previously considered sterile, such as the female upper genital tract. The involvement of these microorganisms in normal physiological processes remains unclear. However, the specific microbiota in the female upper genital tract is strongly correlated with the development of various female diseases. This article reviews the research progress in the microbiota of the female upper genital tract and its associations with normal physiology and genital tract diseases.