Objective <p>The quality and quantity of respiratory muscles directly affect respiratory function, but it’s unclear how much improved muscle function enhances cough capacity. Our preliminary studies show that active/passive lower limb training can improve cough capacity, but the impact of upper limb training is uncertain. This study aims to evaluate the effectiveness of passive upper limb training on cough capacity in long-term tracheostomy patients.</p> Methods <p>In this single-center, single-blind, randomized crossover trial, a total of 27 tracheostomized patients with traumatic brain injury or stroke were enrolled. Participants were randomly allocated into three groups: the CA group (active–passive cycling (APC)/ additional physical therapy (PT) training (APTT) sequence) (<i>n</i> = 11); the AC group (APTT/APC sequence) (<i>n</i> = 10); and the control group (<i>n</i> = 6) (after adjusting for baseline differences using propensity score matching, the control group was reduced from 11 to 6 participants). The APC and APTT interventions were administered for 40&#xa0;min per session, six times per week, over a period of two weeks, in conjunction with standard rehabilitation (SD). The control group received SD for the 14 days. Assessment metrics included the Barthel Index (BI), ultrasound evaluation of respiratory muscle thickness, and Cough Peak Flow (CPF), measured at baseline, after 7 days, and upon completion of the intervention. Comparative analyses were conducted to evaluate the effects during and following the intervention period.</p> Results <p>After adjusting for baseline data, no significant differences were found between groups. While overall APC and APTT periods were similar across groups, the CA group showed significant improvements in the 5th intercostal muscle (ICM), diaphragm, and rectus femoris (RF) during the later intervention phase, with the most notable improvements in the left-sided 2nd and 5th ICM. Overall CPF remained consistent between and within groups, but its increase in the later phase was positively linked to earlier and concurrent increases in the thickness of the 5th and 2nd ICM and the diaphragm.</p> Conclusion <p>This study found no significant improvement in cough capacity from active-passive upper limb training compared to controls. However, it did show increased thickness in respiratory muscles like the intercostals and diaphragm in the intervention groups. This suggests that while APC training aids respiratory muscle adaptation, it doesn’t directly enhance cough capacity. APC training performed similarly to APTT, indicating its potential as a supportive strategy for respiratory conditioning, but it is less effective than lower limb training for improving cough capacity. Future research with longer interventions, resistance, or greater motion range may be needed for meaningful cough function improvements.</p> Trial registration <p>Chinese Clinical Trial Registry (ICTRP member): ChiCTR2500104415. Date of Registration on June 17, 2025.</p>