Objective: To explore the diagnostic value of metagenomic next-generation sequencing (mNGS) on patients with suspected pulmonary tuberculosis accompanied by atypical imaging manifestations and the value in identifying mixed infection. Methods: The data of 200 patients with atypical CT features and negative sputum smear in the hospital from July 2024 to June 2025 were selected for retrospective analysis. According to the final diagnosis, the patients were categorized into pulmonary tuberculosis group (n=124) and non-pulmonary tuberculosis group (n=76). The diagnostic efficiency of bronchoalveolar lavage fluid mNGS, sputum culture and CT features on pulmonary tuberculosis was compared, and the detection rates of pulmonary tuberculosis mixed infection and non-tuberculosis pathogens by mNGS were analyzed. Results: There were no significant differences in hemoptysis/blood sputum, cough, fever, night sweats and weight loss between the pulmonary tuberculosis group and the non-pulmonary tuberculosis group (P>0.05). The incidence rate of localized lesions in the basal segment of the middle and lower lobes, simple miliary nodules and thin-walled cavity in the pulmonary tuberculosis group were higher than those in the non-pulmonary tuberculosis group (P<0.05) while the incidence rates of unilateral pleural effusion with pleural thickening and ground-glass opacity with air bronchogram were lower (P<0.05). The sensitivity, specificity and accuracy rate of mNGS in the diagnosis of pulmonary tuberculosis were 71.77%, 94.74% and 80.50%, respectively, and the consistency Kappa value with the final diagnosis was 0.616. In the pulmonary tuberculosis group, 31 cases of mixed infection were detected, with a detection rate of 25.00%. In the non-pulmonary tuberculosis group, mNGS identified pathogens in 50 cases, with a detection rate of 65.79%. Conclusion: Bronchoalveolar lavage fluid mNGS can improve the diagnostic specificity of atypical pulmonary tuberculosis, and efficiently identify mixed infection and pathogens such as non-tuberculous mycobacteria, providing a basis for accurate anti-infection.