Background Understanding the acute effects of inspiratory muscle training (IMT) at different intensities on the autonomic nervous system, arterial stiffness, and blood pressure in healthy young people will be important in the constitution of appropriate IMT prescriptions. Aims To investigate the acute effects of IMT at different intensities on autonomic function, arterial stiffness, and blood pressure in healthy young people Methods Thirty-six healthy participants were enrolled in this crossover study. All participants randomly performed IMT sessions, which consisted of diaphragmatic breathing exercise (DBE), 10%, 30%, and 60% of maximal inspiratory pressure (MIP) on consecutive days. Autonomic function and arterial stiffness were assessed by measuring heart rate variability (HRV) and aortic pulse wave velocity (AoPWV), respectively. HRV, AoPWV, and blood pressure were recorded before and immediately after each IMT session. Results There was no significant difference in the baseline measurements between IMT sessions (p > 0.05). Heart rate (HR) significantly decreased after DBE and IMT at 10% of MIP (p < 0.05). All time domain parameters of HRV significantly improved after DBE compared with the baseline (p < 0.05). There was no difference in the frequency domain of HRV after the IMT sessions (p > 0.05). AoPWV significantly increased after IMT at 60% of MIP (p < 0.05). Mean arterial pressure significantly changed after DBE and IMT at 60% of MIP (p < 0.05). Conclusions A single session of DBE positively affects autonomic function and blood pressure, while IMT at 60% of MIP increases arterial stiffness. The different intensities of IMT have various impacts on autonomic function, arterial stiffness, and blood pressure.