This study used heart rate variability (HRV) to monitor levels of cancer-related fatigue (CRF) and quality of life (QOL) of cancer survivors subjected to program measures at different psychosomatic or functional levels. A longitudinal study was conducted at a cancer center in Taiwan. Fifty-two cancer survivals were randomly assigned to either the mindfulness group (n = 25) or the Qigong group (n = 27). Both groups received a 12-week mindfulness and Qigong programs, respectively. Improvements in CRF, QOL, and HRV after a 12-week program and at the 3-month follow-up point. For the long-term effects in both mindfulness and Qigong groups, CRF showed a significant downward trend (p < 0.05), but a significant upward trend was observed in HRV (p < 0.001). Mindfulness and Qigong exhibited different effectiveness in individuals, indicating that the mental and physical aspects of health are equally essential and should be addressed in a complementary combination. These findings are worthy of being shared with cancer survivors to benefit their physical and mental well-being. We suggest that healthcare professionals incorporate mindfulness and Qigong in cancer survivors\' daily life as means to encourage lifestyle changes for improving their health.