Gynecological malignancies, such as cervical cancer, ovarian cancer, and endometrial cancer, are characterized by a high degree of heterogeneity. Once they enter the advanced stage, the prognosis is often poor. The emergence and development of single-cell sequencing technology have provided a better platform for investigating the mechanisms of tumor initiation and progression, identifying rare cells, initiation cell lineages, guiding targeted precision therapies for tumors, and predicting patient outcomes at the single-cell level. This article provides a comprehensive review of the rise and development of single-cell sequencing technology and its applications in the research on gynecologic malignancies.