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Mind–body exercise has been proposed to confer both physical and mental health benefits. However, there is no clear consensus on the neural mechanisms underlying the improvements in health. Herein, we conducted a systematic review to reveal which brain region or network is regulated by mind–body exercise. PubMed, Web of Science, PsycINFO, SPORTDiscus, and China National Knowledge Infrastructure databases were systematically searched to identify cross-sectional and intervention studies using magnetic resonance imaging (MRI) to explore the effect of mind–body exercise on brain structure and function, from their inception to June 2020. The risk of bias for cross-sectional studies was assessed using the Joanna Briggs Institute (JBI) checklist, whereas that of interventional studies was analyzed using the Physiotherapy Evidence Database (PEDro) scale. A total of 15 studies met the inclusion criteria. Our analysis revealed that mind–body exercise modulated brain structure, brain neural activity, and functional connectivity, mainly in the prefrontal cortex, hippocampus/medial temporal lobe, lateral temporal lobe, insula, and the cingulate cortex, as well as the cognitive control and default mode networks, which might underlie the beneficial effects of such exercises on health. However, due to the heterogeneity of included studies, more randomized controlled trials with rigorous designs, similar measured outcomes, and whole-brain analyses are warranted.