Early and accurate detection and identification of pathogenic microorganisms are of vital significance for the epidemiological surveillance, prevention, control and treatment of infectious diseases. Compared with traditional approaches, next-generation sequencing technology (NGS) holds remarkable advantages. On one hand, it features a faster and more accurate detection speed, reducing the diagnostic duration. On the other hand, NGS can not only identify pathogens but also further characterize the microbiome and detect resistance genes as well as virulence factors. Hence, it plays a crucial role in the diagnosis, treatment, prevention and control of infectious diseases, particularly in the field of respiratory infectious diseases that may cause widespread dissemination. This article briefly presents NGS technology and its current applications in the diagnosis and treatment of infectious diseases, along with its prospects for future usage