Brain-computer Interfaces (BCIs) provide a direct pathway between the brain and the outward environment. Specifically, motor imagery (MI)-based BCI controlling functional electric stimulation (FES) is a promising approach for disabled patients with intact mind to restore or rehabilitate their motor functions. This study probed for the improvement of cortical activation for motor imagery during the closed-loop BCI-FES training. We used electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS) to inspect the cortical activation for four different training strategies, i.e. MI-BCI-FES, MI-FES, MI and FES. Compared with the other three training conditions, the MI-BCI-FES could achieve stronger cortical activation viewing from the event-related desynchronization (ERD) and the blood oxygen response. The results demonstrate that the closed-loop MI training using BCI-FES can prospectively increase the cortical activation of motor cortical areas.