Previous studies have shown that motor recovery of stroke can be assessed by the cortical activity and the structural integrity of the corticospinal tract (CST), but little is known about the relation between the cortical activity and the structural integrity during motor recovery. In the present study, we investigated the changes in brain activities evoked by twenty days’ functional electrical stimulation (FES) training in twelve sub-acute stroke patients with unilateral upper-limb disability. We compared cortex activity evoked by wrist movement of eleven stroke patients to that of eleven age-matched healthy subjects to figure out how cortex activity changed after stroke. We also measured the structural integrity represented by the fractional anisotropy (FA) asymmetry of the posterior limb of the internal capsule (PLIC) to find the relationship between the brain activity and the structure integrity. In our study, we found that patients with sub-acute stroke have shown greater activity in the contralesional primary motor cortex (M1) during the affected hand’s movement compared with healthy group, while the activity in ipsilesional M1 was decreased after the therapy compared to that before therapy, and the contralesional non-primary motor cortex showed greater activity after therapy. At the baseline we found that the positive correlation between the FA asymmetry of PLIC and the contralesional non-primary motor cortex activity showed that the greater damaged CST, the greater contralesional non-primary motor cortex recruited. While the negative correlation between them after the FES training indicates that after recovery the non-primary motor cortex plays different role in different stroke phases. Our study demonstrates that functional organization of a residual distributed motor system is related to the degree of disruption to the CST, and the non-primary motor areas plays an important role in motor recovery.