The fever of patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is complex, and it is still challenging to identify the cause of the fever. The immune environment after transplantation is more complex. An early correct diagnosis is of great significance to the survival of patients after transplantation. Next-generation sequencing (NGS) has been successfully used to detect novel and rare infections. This study provides a new thought to help the accurate and timely diagnosis of the fever causes after allo-HSCT.