BACKGROUND: Magnetic Seizure Therapy (MST) is an emerging psychiatric physical therapy in recent years, and the MST technique induces seizures by stimulating the local cortex. Numerous studies have shown that compared to electroconvulsive therapy (ECT), magnetic shock therapy (MST) has relatively little effect on cognitive function, and thus has certain advantages in clinical application. However, as far as magnetic shock therapy itself is concerned, there are few studies specifically focusing on its efficacy in depth, and the mechanism of MST in treating schizophrenia is still unclear. METHODS: This study centered on the key question of "the efficacy of magnetic stunning therapy for patients with schizophrenia and the combined fMRI-EEG to explore the regulatory mechanisms of brain networks". The study protocol describes our interventional clinical trial aimed at developing magnetic convulsive therapy as an effective and safe treatment for SCZ. The study population consisted of SCZ patients and healthy controls (Hc). Clinical symptoms, cognitive function, EEG and fMRI data were collected from the patient group at baseline, post-treatment and follow-up phases. We systematically assessed the clinical features and cognitive functions of the patients, combined with EEG and fMRI indexes to explore the brain network connectivity abnormalities in SCZ patients, and jointly explored the neuroimaging mechanisms in SCZ patients. CONCLUSION: Positive results from this trial may have a direct and significant impact on patients with SCZ. Once the MST demonstrates significant antipsychotic efficacy with high perceived safety, it will have significant implications for clinical practice. Brain network abnormality may be one of the core pathological mechanisms of SCZ. Therefore, by combining neurophysiological imaging techniques to scientifically verify the abnormality of SCZ brain network, the elucidation of this issue can help to further reveal the pathological mechanism of SCZ and provide a scientific basis for the effective and precise treatment of the disease. TRIAL REGISTRATION: ChiCTR2000038361 Registered on September 21, 2020.