Objective To explore the application value of pathogen-targeted next-generation sequencing (tNGS) technology in patients with suspected pulmonary infections. Methods A retrospective analysis was conducted on the clinical data of 80 patients with suspected pulmonary infections admitted to the Department of Respiratory and Critical Care Medicine at the Third People's Hospital of Hubei Province from January 2021 to July 2023. All patients underwent bronchoalveolar lavage fluid (BALF) tNGS and conventional pathogen detection. Demographic characteristics of the patients were analyzed, and the distribution of pathogens detected by tNGS and conventional methods were compared. The clinical data of patients diagnosed with single pulmonary infections and those with mixed infections were also compared. Results Among the 80 patients, 74 were diagnosed with infections. Most of the infected patients had underlying conditions, mainly chronic heart disease (42.5%), chronic respiratory disease (35%), and diabetes (20%). The tNGS test results led to changes in treatment strategy for 35 patients (43.8%). A total of 45 types of pathogens were detected, with 169 strains identified by tNGS and 63 strains by conventional methods. Within pathogens detected by both methods, bacteria were detected the most. The order of pathogen types detected by tNGS was bacteria > viruses > fungi > atypical pathogens > Mycobacterium tuberculosis. The order of pathogen types detected by conventional methods was fungi > viruses > bacteria > atypical pathogens > Mycobacterium tuberculosis. The consistency between the two pathogen detection methods was poor (kappa value 0.172, P=0.020). The number of positive cases and the positive detection rates for bacteria, viruses, and atypical pathogens detected by tNGS were significantly higher than those of conventional methods (P<0.05), but there was no statistically significant difference in the positive detection rates for fungi and Mycobacterium tuberculosis between the two methods (P>0.05). Using clinical diagnosis as the gold standard, the sensitivity of tNGS detection was significantly higher than that of conventional methods (P=0.026), while there was no statistically significant difference in specificity between the two methods (P>0.05). Among the 74 confirmed pulmonary infection cases, 6 had no clear pathogen, 23 had single infections, and 45 had mixed infections. Among the mixed infections, the most common combination was bacterial-viral mixed infections (12/45, 26.7%). The mortality rate and hospitalization duration of patients with mixed infections were significantly higher than those with single infections (P<0.05); there were no statistically significant differences in gender, age, underlying conditions, white blood cell count, and neutrophil percentage between the two groups (P>0.05). Conclusions tNGS technology has higher pathogen detection sensitivity compared to conventional methods, especially for bacteria, viruses, atypical pathogens, and rare pathogens. This technology is beneficial for identifying mixed infections and can serve as a supplement to conventional pathogen detection methods in clinical practice.