Objective: To explore the value of nucleic acid detection of pathogenic bacteria in lower respiratory tract in the diagnosis of lower respiratory tract infection. Methods: Patients who underwent nucleic acid testing and bacterial culture for lower respiratory pathogens from December 2023 to November 2024 were selected as subjects. The detection rates of respiratory pathogens by both methods were compared. Results: For six common pathogens causing lower respiratory infections, the positive detection rate of nucleic acid testing was significantly higher than that of conventional bacterial culture (69.68% vs.20.88%). For Pseudomonas aeruginosa, the two methods had good consistency in positive detection rates (Kappa=0.644, P＜0.001), while the consistency of detection rate of klebsiella pneumoniae between the two methods was general (Kappa=0.473, P＜0.001), and that of staphylococcus aureus was poor (Kappa=0.287, P＜0.001). The average turnaround time within the laboratory for nucleic acid testing was 4.68 hours, while that for conventional bacterial culture was 49.75 hours, the average turnaround time of nucleic acid detection in the laboratory was significantly lower than that of bacterial culture (P＜0.001). Conclusion: Nucleic acid detection of pathogenic bacteria in lower respiratory tract has more advantages in rapid identification of pathogenic bacteria in respiratory tract, with shorter laboratory turnaround time, can provide timely information on pathogenic bacteria for clinicians, and has higher clinical significance for patients with severe and rapid progress.