Objective: To investigate the preventive effects of early pulmonary rehabilitation training on ventilator-induced diaphragmatic dysfunction (VIDD) in ICU mechanically ventilated patients and its impact on clinical outcomes. Methods: A prospective randomized controlled trial was conducted. A total of 82 mechanically ventilated patients admitted to the intensive care unit of a tertiary hospital from January 2025 to December 2025 were enrolled and randomly assigned to either the experimental group (n = 41) or the control group (n = 41) using a random number table. The control group received routine ICU care and an early mobilization protocol, while the experimental group received systematic early pulmonary rehabilitation training in addition to the control protocol. Ultimately, 75 patients completed the study. Diaphragm excursion (DE), diaphragmatic thickening fraction (DTF), maximum inspiratory pressure (MIP), duration of mechanical ventilation, ICU length of stay, incidence of VIDD, and adverse events were compared between the two groups. Results: On day 5 and day 7 of the intervention, DE and DTF in the experimental group were significantly higher than those in the control group (p < 0.05). MIP on day 7 was significantly higher in the experimental group than in the control group (p < 0.001). The experimental group had significantly shorter durations of mechanical ventilation (6.2 ± 2.1 days vs. 8.7 ± 3.4 days) and ICU stays (9.5 ± 3.2 days vs. 12.8 ± 4.6 days) compared to the control group (p < 0.001). The incidence of VIDD was significantly lower in the experimental group (15.8%, 6/38) than in the control group (40.5%, 15/37; p = 0.017). No significant difference was found in the incidence of adverse events between the two groups (p > 0.05). Conclusion: Early pulmonary rehabilitation training effectively improves diaphragmatic function, reduces the incidence of VIDD, shortens the duration of mechanical ventilation and ICU length of stay in mechanically ventilated patients, and demonstrates good safety.