In acute or chronic lung diseases, inappropriate immune response and abnormal repair process can lead to irreversible damage to lung tissue, which in turn leads to decreased lung function and even respiratory failure or death. Mesenchymal stem cells (MSCs) and their derivatives have shown wide application prospects in cell therapy and acellular therapy of lung diseases and are entering the clinical transformation stage because of their unique physiological functions and characteristics, but the safety and efficacy of MSCs and their derivatives are still controversial. Nebulization therapy provides new opportunities and challenges for the innovative treatment of MSCs and their derivatives in lung diseases. In a number of preclinical studies and clinical trials, there have been evidence that atomization therapy of MSCs and their derivatives is safe and effective. This method could be an optimal solution for the treatment of various complex lung diseases. However, extensive research should be carried out on various strategies and their compatibility with different nebulizers before this method can be used in clinical setting. In this paper, we review the research progress of MSCs and their derivatives by nebulization in the treatment of pulmonary diseases.