This study aims at comparing the effects of the Baduanjin mind-body (BMB) intervention with a conventional relaxation training program on enhancing the executive function. The study also attempts to explore the neural substrates underlying the cognitive effect of BMB intervention using near-infrared spectroscopy (NIRS) technique. Forty-two healthy college students were randomly allocated into either the Baduanjin intervention group or relaxation training (control) group. Training lasted for 8 weeks (90 min/day, 5 days/week). Each participant was administered the shortened Profile of Mood States to evaluate their mood status and the flanker task to evaluate executive function before and after training. While performing the flanker task, the NIRS data were collected from each participant. After training, individuals who have participated in BMB exercise showed a significant reduction in depressive mood compared with the same measure before the intervention. However, participants in the control group showed no such reduction. The before vs. after measurement difference in the flanker task incongruent trails was significant only for the Baduanjin intervention group. Interestingly, an increase in oxygenated hemoglobin in the left prefrontal cortex was observed during the Incongruent Trails test only after the BMB exercise intervention. These findings implicate that Baduanjin is an effective and easy-to-administering mind-body exercise for improving executive function and perhaps brain self-regulation in a young and healthy population.