Organ transplantation is a critical treatment for end-stage organ diseases, yet postoperative infections significantly affect patient outcomes. Traditional diagnostic methods for infections often fall short in meeting the demands of precise prevention and treatment due to limitations in sensitivity, specificity, and speed. Targeted nanopore pathogen sequencing technology, characterized by its long-read capability, real-time detection, and adaptability, has shown unique potential in pathogen identification, structural variation analysis, and antimicrobial resistance gene profiling. This offers new insights into the prevention and management of postoperative infections. This expert consensus focuses on the standardized application of this technology in managing infections following organ transplantation, addressing its principles, clinical recommendations, and diagnostic workflows. By exploring its features and value in infectious disease diagnosis, the expert consensus provides standardized guidance on sample processing and result interpretation. The development of this consensus aims to promote the rational use of nanopore sequencing in diagnosing and treating post-transplant infections, enhance diagnostic accuracy and efficiency, improve patient outcomes, and facilitate the widespread adoption of this technology.