Malignant cancer is a kind of fatal disease with severe threat to human health and social development, and seeking a scientific method for the proper diagnosis, treatment and assessment has become one of the most important public health problems in recent years. With the constant development in healthcare industry, traditional methods of tumor screening, prevention and prognosis assessment have made a rapid progress. However, owing to the characteristics of tumor heterogeneity and patient individuation, precision medicine mode in disease screening, diagnosis and treatment will become a general trend in future medical development. As an important part in precision medicine, gene variation detection in the field of tumors involves several aspects, including early screening, recurrence monitoring, guidance on use of targeted drugs and assessment of efficacy and prognosis etc; However, there are still many limitations in its clinical practice. Therefore, further research is needed to promote the development of tumor precision medicine. In this paper, the development history of gene variation detection and its application progress in precision medicine of malignant tumors are comprehensively discussed.