<p>With the continuous development of molecular biotechnology, a new pathogen detection method, next generation sequencing (NGS), has been gradually applied to the clinic, and there are two main types: macrogenomic next generation sequencing (mNGS) and targeted next generation sequencing (tNGS). mNGS sequences a mixture of all DNA or RNA of the sample to be tested and obtains taxonomic information on the pathogen by comparing the sequencing data with a pathogen database, allowing for the unbiased detection of all microbiomes, drug resistance markers, virulence factors, and even hosts associated with different disease states. tNGS employs a selection process to enrich microbial sequences of interest prior to library preparation and sequencing, with the advantage of overcoming the “needle in the haystack” dilemma of amplifying a small number of microbial sequences in a highly cellular sample. NGS technology has emerged, which has great potential for the diagnosis of lung infectious disease pathogens, especially in the field of conventional detection methods with limitations. In this paper, we summarize the current status, advantages, and disadvantages of mNGS and tNGS technologies in the detection of lung infectious pathogens, with reference to the latest research developments at home and abroad, to serve as a reference for the clinical diagnosis and treatment of respiratory infections.</p>