This study evaluated the diagnostic utility of ultra-multiplex polymerase chain reaction(PCR)-based targeted next-generation sequencing (tNGS) in invasive pulmonary aspergillosis (IPA). A cohort of 209 patients clinically suspected of IPA during May and July 2023 underwent bronchoalveolar lavage fluid (BALF) collection via fiberoptic bronchoscopy. Samples were analyzed using tNGS, galactomannan (GM) assay, and Gram-stained smear. Among 209 suspected IPA cases, tNGS identified Aspergillus in 183 samples, achieving an 87.6% positivity rate. Aspergillus fumigatus was the predominant species (69.4%), followed by Aspergillus flavus (23.5%), Aspergillus terreus (3.83%), and Aspergillus niger (3.3%). GM assay, using a BALF GM index cutoff of ≥1.0, yielded a significantly lower positivity rate of 70.3% (P<0.001), but both outperformed Gram-stained smear (20.1%). Co-detection of other pathogens occurred in 168 tNGS-positive samples (91.8%). Notably, tNGS-derived Aspergillus read counts were significantly higher in GM-positive versus GM-negative patients (P<0.001). Among 15 583 BALF samples analyzed in 2023, tNGS identified Aspergillus in 2 131 (13.7%) samples. Co-pathogens were detected in 91.1% of Aspergillus-positive cases, with influenza virus (25.9%), Klebsiella pneumoniae (14.2%), Acinetobacter baumannii (12.6%), SARS-CoV-2 (12.1%), and Pseudomonas aeruginosa (9.53%) being the predominant other pathogens. This study demonstrates that tNGS surpasses the GM assay in both sensitivity and specificity for IPA diagnosis, enables precise Aspergillus species identification, and excels in detecting fungal co-infections.