Nanopore sequencing technology, featured by its long read lengths, real-time analysis, direct sequencing, and high portability, shows great potential in pathogen diagnosis and precision medicine. However, its clinical translation is still limited by deficiencies in the standardization of experimental protocols, data analysis pipelines, and the consistency of result interpretation. Based on recent research and evidence-based medicine, this consensus elaborates on the appropriation scope and technical normative requirements of nanopore sequencing technology from 3 aspects: rapid detection of pathogenic microorganisms, application in precision diagnosis, and establishment of standardized procedures and quality control. It clarifies the key value of this technology in the diagnosis of acute and critical infections, detection of microbial resistance genes, methylation analysis, and identification of large nucleic acid fragment variations. Recommendations and prospects are also proposed for laboratory conditions, experimental operations, and bioinformatics analysis processes, aiming to promote the innovation and rational application of nanopore sequencing technology.