Abstract: Traditional microbial detection methods have difficulty meeting the needs of pathogen detection in the clinic. In recent years, metagenomic next-generation sequencing (mNGS) technology has emerged and been widely used in the diagnosis of various infectious diseases, the etiological analysis of emerging infectious diseases, the detection of drug resistance genes and the analysis of the host immune response. However, the mNGS workflow is complicated, and the variation introduced in each step will influence the accuracy of the detection results. In addition, the absence of standardized methods, the lack of personnel knowledge and ability, and the high cost of instruments and reagents are also creating main obstacles to the clinical application of mNGS. Therefore, standardization and normalization of methods as well as improvement of personnel knowledge and ability are urgently needed for mNGS detection. The integration of pathogen, transcriptome and antibiotic resistance genes information to comprehensively improve the clinical management of patients with infectious diseases is an important direction of mNGS detection.