Objective To investigate the efficacy of matrix assisted laser desorption/Ionization ⁃ time of flight mass spectrometry（MALDI⁃TOF MS）for the diagnosis of smear⁃negative or sputum⁃scarce pulmonary tuber⁃ culosis（PTB）by testing bronchoalveolar lavage fluid（BALF）. Methods BALF of 87 patients with suspected smear⁃negative or sputum⁃scarce tuberculosis were tested by MALDI⁃TOF MS，SAT⁃TB，Gene⁃Xpert and BD960 from January 2020 to December 2021 in Anhui Chest Hospital. The results from those methods were compared. Results The sensitivity of MALDI⁃TOF MS for diagnosing smear⁃negative or sputum⁃scarce PTB was 68.5%（37/ 54），which was better than that of SAT⁃TB 13.0%（7/54），or Gene⁃Xpert 40.7%（22/54），or BD960 27.8%（15/54） （all P < 0.01）. The AUC value of MALDI⁃TOF MS was 0.827，which was better than that of SAT⁃TB 0.550，or Gene ⁃Xpert 0.704，or BD960 0.639（all P < 0.01）. Combining MALDI ⁃TOF MS with any one of the other three methods did not produce a better AUC value than using it alone. Conclusion MALDI⁃TOF MS appears to be a more accurate method in assisting the diagnosis of smear⁃negative or sputum⁃scarce PTB.