In recent years, due to the extensive usage of immunosuppressant and the rise of patients with cancers and organ transplantation, the incidence rate of invasive fungal infection, especially invasive pulmonary fungal infection, has increased. Besides the clinical manifestations, medical history and imaging, the diagnosis of pulmonary mycosis mainly depends on pathogen detection methods in clinical microbiology laboratory. However, due to the difficulty in fungi culturing and the low sensitivity of smear microscopy, better molecular biology methods are needed. To date, the emergence of metagenomic next-generation sequencing (mNGS) has improved the identification rate of pulmonary fungal infections. mNGS is significantly superior to traditional detection methods in rapid, accurate, and comprehensive determination of fungi from various clinical specimens, especially atypical fungi. However, some problems in mNGS method have to be addressed including sample collection, report interpretation, and its combination with traditional microbiology methods. With the in-depth discussion and solution of the above problems, mNGS will be indispensable to the etiological diagnosis of pulmonary invasive fungal infection.