Stroke causes abnormality of brain physiological function and limb motor function. Brain-computer interface (BCI) connects the patient's active consciousness to an external device, so as to enhance limb motor function. Previous studies have preliminarily confirmed the efficacy of BCI rehabilitation training in improving upper limb motor function after stroke, but the brain mechanism behind it is still unclear. This paper aims to review on the brain mechanism of upper limb motor dysfunction in stroke patients and the improvement of brain function in those receiving BCI training, aiming to further explore the brain mechanism of BCI in promoting the rehabilitation of upper limb motor function after stroke. The results of this study show that in the fields of imaging and electrophysiology, abnormal activity and connectivity have been found in stroke patients. And BCI training for stroke patients can improve their upper limb motor function by increasing the activity and connectivity of one hemisphere of the brain and restoring the balance between the bilateral hemispheres of the brain. This article summarizes the brain mechanism of BCI in promoting the rehabilitation of upper limb motor function in stroke in both imaging and electrophysiology, and provides a reference for the clinical application and scientific research of BCI in stroke rehabilitation in the future.