Brain activation during motor imagery has been studied extensively for years, but only a few of these studies focused on investigating the effective connectivity in the brain. The existence of interactions or closed loop circuits between the SMA and other brain regions during motor imagery still remains unclear. In the present study, selecting the SMA as the region of interest, we used the Granger causality mapping (GCM) method to explore the effective connectivity in the brain during motor imagery. Our results demonstrated that more brain regions showed effective connections to the SMA during the right-hand motor imagery than during the left-hand motor imagery, but the strength of the casual influence during the left-hand motor imagery was stronger than that of the right-hand motor imagery. We further found forward and backward effective connectivity between the SMA and three regions, including the bilateral dorsal premotor area (PMd), the contralateral primary and secondary somatosensory cortex (S1), and the primary motor cortex (M1). these results might indicate how the brain regions were inter-activated during motor imagery.