Objective To analyze strain distribution and clinical characteristics of non-tuberculous mycobacterial (NTM) pulmonary disease (NTM-PD) in Fuzhou City, provide reference and evidence for clinical diagnosis and treatment of NTM-PD. Methods Medical records of patients who were isolated Mycobacteria from culture of sputum or bronchoalveolar lavage fluid (BALF) specimens sent by Fuzhou Pulmonary Hospital of Fujian Province between January 2018 and January 2020 were analyzed retrospectively. Strain distribution and relevant clinical characteristics of patients with NTM-PD were analyzed. Results A total of 249 patients were confirmed with NTM-PD, 10 cases (4.0%) were co-infection of NTM and Mycobacterium tuberculosis. Among 249 patients with NTM-PD, the middle-aged and elderly were more common, and women were slightly more than men. The most common pathogen was Mycobacterium intracellulare (60.6%, 151 strains), followed by Mycobacterium avium (17.7%, 44 strains) and Mycobacterium chelonae/Mycobacterium abscessus (17.7%, 44 strains). The common susceptible factors for NTM-PD were bronchiectasis (70.3%, n=175), history of tuberculosis (28.5%, n=71), pneumoconiosis (14.5%, n=36), chronic obstructive pulmonary disease (COPD) (11.2%, n=28), history of tumor (4.8%, n=12), and diabetes mellitus (4.4%, n=11). Men were more likely to be complicated with COPD and women were more likely to be complicated with bronchiectasis. Clinical symptoms of NTM-PD were nonspecific, often manifested as cough, expectoration, hemoptysis, chest tightness and pain, shortness of breath, fever and so on, there is no correlation between clinical symptoms and species, but shortness of breath and hemoptysis were correlated with gender, men were more likely to have shortness of breath, while women were more likely to have hemoptysis. Pulmonary nodule was the most common imaging manifestation of NTM-PD, accounting for 90.8%; followed by bronchiectasis and pulmonary cavity, accounting for 70.3% and 62.7% respectively. NTM-PD was easily misdiagnosed as pulmonary tuberculosis (68.3%) and bronchiectasis (16.9%), the cure rate was low (34.6%). Conclusion Clinical symptoms and imaging manifestations of NTM-PD and pulmonary tuberculosis are very similar, which is easy to be misdiagnosed. For patients with history of tuberculosis, bronchiectasis, COPD, pneumoconiosis, diabetes mellitus and low immunity, those who are with pulmonary nodules, bronchiectasis and pulmonary cavity should be highly alert to the possibility of NTM-PD, timely and accurate identification of pathogen should be conducted to guide clinical treatment.