Purpose The importance of supplementary motor area (SMA) for motor function and compensation for primary motor area (M1) has received increased attention. Methods We used diffusion tensor imaging (DTI) and transcranial magnetic stimulation (TMS) to evaluate structure and function of corticospinal projection originating from SMA. Fibers of corticospinal projection originating from M1 (CST) and SMA (ACST) were analyzed. ACST originating from mesial SMA area formed separate white matter bundles leaving the anterior part of M1 area, which then entered the posterior limb of the internal capsule. Projection and overlap of both CST and ACST were detected on medulla. Results Fibers of contralesional ACST were more than that of ipsilesional ACST in patients with SMA tumors ( p <0.05). In patients with SMA tumor, all patients experienced temporary akinesia postoperatively. Seven hundred forty-one fibers of ipsilateral ACST and no fibers of ipsilateral CST were detected in the patient with M1 glioma, while most of contralateral limb movement was preserved. MEP could be evoked by stimulating SMA area as well as M1 area. ACST originated from SMA area and projected to the medial medulla. Conclusion SMA area and ACST integrity contributed to contralateral motor function and were a compensation for M1 lesion and damaged CST.