Abstract: Objective To explore the clinical value of metagenomic next-generation sequencing (mNGS) in the pathogen spectrum analysis of acute exacerbations in interstitial lung disease (AE-ILD).Methods The medical records of AE-ILD patients who admitted to the Affiliated Hospital of Xuzhou Medical University from June 2020 to June 2022 were retrospectively analyzed. We included 85 AE-ILD patients who underwent pathogen testing using both conventional microbiological methods and mNGS, inorder to analyze the distribution of pathogens and the presence of co-infections in these patients. Based on the 90-day survival outcome, AE-ILD patients were divided into a survival group (54 cases) and a death group (31 cases), and the differences in pathogens between the two groups were compared.Results Among the 85 AE-ILD patients, a total of 88 pathogens were detected using mNGS, with viruses being the most common (41.78%), followed by bacteria (37.47%) and fungi (20.75%). Approximately 70.59% of patients exhibited co-infections, with the most common type being virus + fungi +bacteria (55.01%). The overall mortality rate of AE-ILD patients was 32.94% at one month and 36.47% at three months after admission. Notably, the detection rates of human herpesvirus type 1, human herpesvirus type 7, and Pneumocystis jirovecii were significantly higher in the death group compared to the survival group.Conclusions The common pathogens detected by mNGS technology in AE-ILD patients include Epstein-Barr virus, cytomegalovirus, Candida albicans, HHV-1, HHV-7, Streptococcus pneumoniae, and Pneumocystis jirovecii. The high occurrence of co-infections highlights the significance of respiratory infections as a common trigger for AE-ILD.