BACKGROUND: The goal of this study was to investigate treatment outcome and related intervention processes of mindfulness-based cognitive therapy versus health qigong-based cognitive therapy versus waitlist control among individuals with mood disorders. METHODS: A total of 187 individuals with mood disorders were randomized and allocated into mindfulness-based cognitive therapy, health qigong-based cognitive therapy, or waitlist control groups. All participants were assessed at three time points with regard to depressive and anxiety symptoms, physical and mental health status, perceived stress, sleep quality, and self-efficacy. Linear mixed models analysis was used to test the individual growth model by studying the longitudinal data. RESULTS: Mindfulness-based cognitive therapy and health qigong-based cognitive therapy both produced greater improvements on all outcome measures as compared with waitlist control. Relatively, more reductions of mood symptoms were observed in the health qigong-based cognitive therapy group as compared with the mindfulness-based cognitive therapy group. Health qigong-based cognitive therapy is more conducive to physical health status whereas mindfulness-based cognitive therapy has more favorable mental health outcomes. Individual growth curve models indicated that alterations in perceived stress was the common predictor of mood changes in both intervention groups. CONCLUSIONS: The predominant emphasis on physical health in health qigong-based cognitive therapy makes it more acceptable and effective than mindfulness-based cognitive therapy as applied in Chinese individuals with mood disorders. The influence of Chinese culture is discussed. TRIAL REGISTRATION: HKU Clinical Trials Registry. Identifier: HKUCTR-2558 . Registered 21st Nov 2018.