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BackgroundIn Chinese medicine, the mental focus and emotional stability of acupuncturists are key to optimal clinical outcomes. Many renowned acupuncturists utilize Traditional Chinese Qigong practices to enhance their concentration and emotional regulation abilities. Nevertheless, the existing literature lacks comprehensive evidence addressing this matter.MethodsThis study will enroll 99 acupuncturists and randomly allocate them to one of three groups: Baduanjin, aerobic exercise, or a waiting-list control. The Baduanjin group will undertake 24 weeks of training, with three one-hour sessions weekly. The aerobic group will engage in brisk walking for the same duration and frequency. The control group will not receive any specific training. Assessments of emotion regulation, attention, cognitive functions, finger sensation, and athletic ability will be conducted at baseline (−1 week), mid-intervention (12 weeks), and post-intervention (24 weeks). Additionally, 20 participants from each group will undergo fMRI scans before and after the intervention to explore brain functional and structural changes relating to emotion, attention, cognition, motor skills, and sensory perception.DiscussionThis study aims to contribute valuable insights into the effectiveness of Qigong practice, specifically Baduanjin, in enhancing emotional regulation, attention, and cognitive functions in acupuncturists and to investigate the neuroimaging mechanisms behind these effects.Ethics and disseminationApproved by the Sichuan Regional Ethics Review Committee on Traditional Chinese Medicine (No. 2023KL − 118) and adhering to the Declaration of Helsinki. Results will be shared through policy briefs, workshops, peer-reviewed journals, and conferences.Clinical trial registrationwww.chictr.org.cn, ChiCTR2300076447.