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Introduction Chronic insomnia is a pressing public health issue that significantly affects patients’ quality of life. In China, Prolong Life With Nine Turn-Method (PLWNT) Qigong exercise has long been used to improve sleep quality, yet evidence that supports its efficacy for chronic insomnia treatment remains lacking. The aim of this study is to evaluate the effectiveness and safety of the PLWNT qigong exercise for treating chronic insomnia and its relationship with hyperarousal.Methods and analysis This multi-centre randomised controlled trial will recruit 348 eligible patients from three hospitals in Shanghai. Participants will be randomly assigned to either the treatment group (PLWNT qigong exercise) or the control group (cognitive behavioural therapy). The treatment will occur once a week for 12 weeks, followed by an 8-week follow-up phase. The primary outcome is the change in the total Pittsburgh Sleep Quality Index (PSQI) score from baseline to week 12. The secondary outcomes are the scores on the Hyperarousal Scale (HAS), Insomnia Severity Index (ISI), Multidimensional Fatigue Inventory 20 (MFI-20), Hospital Anxiety and Depression (HADS), Medical Outcome Trust 36–Item Short Form Health Survey (SF–36) and Gastrointestinal Symptom Rating Scale (GSRS), gut microbiota, actigraphy, sleep diary, cortisol, adrenocorticotrophic hormone, corticotropin-releasing hormone, polysomnography and functional MRI. All adverse events during the trial will be promptly recorded and assessed. The PSQI, HAS, ISI, MFI-20, HADS, SF–36 and GSRS will be evaluated at baseline, 6 weeks post-treatment and 12 weeks post-treatment, as well as at the 4- week and 8- week follow-ups. Other outcomes will only be evaluated at baseline and 12 weeks post-treatment.Ethics and dissemination The trial has been approved by the Ethics Committee of the Shanghai Municipal Hospital of Traditional Chinese Medicine (2024SHL-KY-92–01). Written informed consent was obtained from all participants before their involvement in the trial. Results of this study will be published in peer-reviewed journals or at conferences.Trial registration number ITMCTR2024000534.