Abstract: Metagenomic next generation sequencing (mNGS) is a non-preference, highly sensitive and highly specific molecular biological detection method. Currently, it is widely used in the auxiliary diagnosis of a variety of infectious diseases in clinical practice, which has greatly improved the survival rate and cure rate of patients. In recent years, there are increasing numbers of reports on the clinical application of mNGS. This article mainly reviews the advantages and challenges in the application of mNGS for diagnosis and treatment of respiratory infectious diseases.