The incidence of respiratory infections is high, and early identification of infectious pathogens is the key to improving clinical results. Metagenomics next-generation sequencing (mNGS) has the advantages of being whole spectrum, time saving, no specific amplification of pathogens, and has high clinical application value in the identification of rare infections, mixed infections, immunosuppressive patient infection and the diagnosis of pathogens that are difficult to be detected by conventional methods. However, mNGS results of some cases have low specificity, lack recognized interpretation standards, have unclear relationships between sequencing results and treatment, and have difficulties testing drug-resistant genes. In clinical application present, mNGS and traditional microbial detection technology have a complementary effect and the combination of the two can improve the clinical diagnosis efficiency.