OBJECTIVE: This longitudinal study aimed to investigate the effects of Qigong on the anxiety state, heart rate variability (HRV), and breathing of anxious college students. METHODS: A total of 37 individuals (18-25 years old) were randomly allocated to the control (n = 19) and intervention (n = 18) groups. Qigong interventions were conducted five times weekly for 12 weeks, with each session lasting 60 min. Hamilton Anxiety Scale, Fatigue Scale 14, Pittsburgh Sleep Quality Index, and 36-item Short Form Survey, HRV, and respiration data were collected before and after the 3-month intervention. RESULTS: Individuals who participated in the three-month Qigong exercise intervention showed a significant reduction in anxiety, particularly mental anxiety (p < 0.05). Subjects in the intervention group presented a decrease in skin temperature (p < 0.05) and an increase in blood volume pulsation (p < 0.05). Meanwhile, HRV exhibited a significant increase in the standard deviation of interbeat interval before and after comparisons (p < 0.05) and between the two groups (p = 0.039) and a reduction in the normalized low-frequency power after the intervention. Moreover, the intervention group experienced increased abdominal breathing depth and abdominal breathing per minute (p < 0.05). CONCLUSION: These findings indicate that Qigong is an effective mind-body exercise strategy for relieving anxiety. HRV and breathing were improved accordingly among college students after the completion of the 3-month Qigong program.