Objective To investigate the application value of pulmonary alveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in the diagnosis of invasive pulmonary aspergillosis (IPA) and analyze the risk factors. Methods We divided 110 suspected IPA patients admitted to the respiratory and critical care department of our hospital from January 2020 to June 2024 into IPA group (n=45) and non-IPA group (n=65) based on the gold standard of clinical comprehensive diagnosis. We analyzed the differences in general clinical data between the two groups and the diagnostic efficacy of conventional methods (BALF and sputum fungal culture and smear examination) and BALF mNGS for IPA; we also explored the effects of mNGS Aspergillus sequence number threshold, chest CT findings, and bronchoscopic findings on the results of BALF mNGS.Results The incidence of diabetes mellitus (28.9% vs 7.7%), imaging air crescent sign (11.1% vs0), and white necrotic material adhering to the airway (13.3% vs 0) were significantly higher in the IPA group than in the non-IPA group (P<0.05). The sensitivity, specificity, positive predictive value, and negative predictive value of BALF mNGS were 84.44%, 90.77%, 86.36%, and 89.39%, respectively, with a Kappa value of 0.755 (P<0.001); the corresponding values for conventional methods were 44.44%, 95.38%, 86.96%, and 71.26%, with a Kappa value of 0.431 (P<0.001). The area under the ROC curve (AUC) was 0.894 (standard error 0.035; 95% CI:0.825~0.962), and the threshold value for Aspergillus sequence number was 5, with a sensitivity of 0.844 and a specificity of 0.908 (P value<0.001). Multivariate analysis showed that the presence of multiple lesions on chest CT and new lesions in the airway were statistically significant factors affecting the detection of Aspergillus by BALF mNGS (P value<0.05). Conclusion BALF mNGS has high diagnostic efficacy for IPA; the optimal cut-off value for Aspergillus sequences is 5, and the probability of detecting Aspergillus infection by BALF mNGS increases with the presence of multiple lesions on chest CT and new lesions in the airway