In recent years, pathogenic metagenomic next-generation sequencing (mNGS) technology has become more and more widely used in the field of clinical infection. Driven by clinical needs, mNGS technology is constantly being optimized and developed. From manual operation to automated process, from simple qualitative detection to quantitative monitoring, from infection identification to multi-dimensional diagnosis of “infection+tumor”, certain research results have been achieved. Of course, there are still some limitations in clinical application of this technology. For example, there are many mNGS detection related reagents in China, but a systematic and complete quality management control and evaluation system has not been established. Further research is needed. This article summarizes the development and application of pathogen metagenomic sequencing technology in recent years, as well as the standardization and normalized process of mNGS detection, in order to provide a reference for pathogen mNGS sequencing to better assist clinical infection diagnosis.