Although rehabilitation exercise is known to be beneficial for cardiovascular and mental health, it remains a daunting challenge for patients with spinal cord injury (SCI) who rely on wheelchairs for mobility. This study aimed to examine the effectiveness of a 4-week para table tennis program in enhancing self-efficacy and health outcomes in adults with SCI. A total of 39 SCI patients were included and divided into the experimental group (n = 18, a 4-week para table tennis training program) and the control group (n = 21). Frequency domain indices of heart rate variability (HRV) were used to evaluate the function of the autonomic nervous system. Following para table tennis training, there was a significant reduction in the physical stress index (PSI, P < 0.001), accompanied by shifts in autonomic regulation of vagal dominance. Additionally, the para table tennis training led to significant improvements in vessel state, differential pulse wave index, atrial elasticity, eccentric constriction power, remaining blood volume, and self-efficacy (all P < 0.05). Para table tennis training results in favorable changes in sympathetic tone, enhanced self-efficacy, improved cardiovascular well-being, and an overall positive transformation in HRV.