Abstract: Metagenomic next generation sequencing (mNGS) based diagnostics that identify microbial nucleic acids in clinical samples may be a useful tool in addressing some of these challenges. Studies of mNGS in immunocompromised hosts have demonstrated that these diagnostics are capable of identifying causative organisms in a subset of patients for whom conventional testing has been negative. But the reports evaluating the diagnostic efficiency of mNGS in immunocompromised patients are limited to individual patients or small retrospective studies at present. This article reviewed and analyzed the literature to provide new ideas for conducting related research on mNGS in clinical practice.