Stroke is one of the most serious diseases that threaten human life and health. It is a major cause of death and disability in the clinic. New strategies for motor rehabilitation after stroke are undergoing exploration. We aimed to develop a novel artificial neural rehabilitation system, which integrates brain--computer interface (BCI) and functional electrical stimulation (FES) technologies, for limb motor function recovery after stroke. We conducted clinical trials (including controlled trials) in 32 patients with chronic stroke. Patients were randomly divided into the BCI-FES group and the neuromuscular electrical stimulation (NMES) group. The changes in outcome measures during intervention were compared between groups, and the trends of ERD values based on EEG were analyzed for BCI-FES group. Results showed that the increase in Fugl Meyer Assessment of the Upper Extremity (FMA-UE) and Kendall Manual Muscle Testing (Kendall MMT) scores of the BCI-FES group was significantly higher than that in the sham group, which indicated the practicality and superiority of the BCI-FES system in clinical practice. The change in the laterality coefficient (LC) values based on μ-ERD (ΔLC_m-ERD) had high significant positive correlation with the change in FMA-UE(r= 0.6093, P=0.012), which provides theoretical basis for exploring novel objective evaluation methods.