The rehabilitation effect of patients with moderate or severe upper limb motor dysfunction after stroke is poor, which has been the focus of research owing to the difficulties encountered. Brain-computer interface (BCI) represents a hot frontier technology in brain neuroscience research. It refers to the direct conversion of the sensory perception, imagery, cognition, and thinking of users or subjects into actions, without reliance on peripheral nerves or muscles, to establish direct communication and control channels between the brain and external devices. Motor imagery brain-computer interface (MI-BCI) is the most common clinical application of rehabilitation as a non-invasive means of rehabilitation. Previous clinical studies have confirmed that MI-BCI positively improves motor dysfunction in patients after stroke. However, there is a lack of clinical operation demonstration. To that end, this study describes in detail the treatment of MI-BCI for patients with moderate and severe upper limb dysfunction after stroke and shows the intervention effect of MI-BCI through clinical function evaluation and brain function evaluation results, thereby providing ideas and references for clinical rehabilitation application and mechanism research.