Respiratory muscle weakness often occurs after stroke, which can lead to pulmonary dysfunction (PD). Pulmonary dysfunction prolongs the length of hospital stay and increases the risk of death. In a prospective, randomized, case-control study, we used musculoskeletal ultrasonography (MSUS), and pulmonary function tester to objectively evaluate the efficacy of repetitive transcranial magnetic stimulation (rTMS) combined with respiratory muscle training (RMT) in the treatment of PD in patients with acute ischemic stroke. Sixty-two stroke patients with PD were recruited and eventually 60 patients participated in this study. The control group was treated with RMT, and the treatment group was treated with rTMS on the basis of RMT. Treatment occurred five times a week for 8 weeks. Before and after treatment, diaphragmatic thickness (DT), diaphragmatic thickening fraction (DTF) and diaphragmatic mobility (DM) in patients, bilateral chest wall were measured by MSUS. Meanwhile, FVC, FEV1, FEV1/FVC, PEF, and MVV tested by pulmonary function tester was used to evaluate the improvement of lung functional. activities of daily living (ADL) was used as an objective criterion to evaluate the overall functional recovery of patients before and after treatment. After treatment, DT, DTF, and DM values improved significantly in both the affected and unaffected sides. The FVC, FEV1, FEV1/FVC, PEF, MVV, and ADL were all increased after the treatment. Combined treatment showed a stronger increase than that by RMT treatment alone. The study preliminarily shows that rTMS and RMT could improve lung functional after acute ischemic stroke.