Brain computer interfaces (BCIs) have been demonstrated to have the potential to enhance motor recovery after stroke. However, some stroke patients with severe paralysis have difficulty achieving the BCI performance required for participating in BCI-based rehabilitative interventions, limiting their clinical benefits. To address this issue, we presented a BCI intervention approach that can adapt to patients' BCI performance and reported that adaptive BCI-based functional electrical stimulation (FES) treatment induced clinically significant, long-term improvements in upper extremity motor function after stroke more effectively than FES treatment without BCI intervention. These improvements were accompanied by a more optimized brain functional reorganization. Further comparative analysis revealed that stroke patients with low BCI performance (LBP) had no significant difference from patients with high BCI performance in rehabilitation efficacy improvement. Our findings suggested that the current intervention may be an effective way for LBP patients to engage in BCI-based rehabilitation treatment and may promote lasting motor recovery, thus contributing to expanding the applicability of BCI-based rehabilitation treatments to pave the way for more effective rehabilitation treatments.