Rapid identification of pathogens is the basis for clinic diagnose and infectious disease prevention and control. High throughput sequencing technology breaks through the limitation of traditional detection methods, such as timeliness and sensitivity, providing an efficient way for clinical detection and research. In this review, the development of high throughput sequencing technology was discussed, mainly by introducing the three-generation nanopore sequencing technology. At the same time, the application of nanopore sequencing technology about the detection and study in viral infectious diseases were reviewed, and the application prospects and possible problems are prospected.