In this study, a structurally constrained susceptibility reconstruction method, SCSWIM, is proposed. This method employs the unique contrast of STAGE imaging and segmented basal ganglia and vessels. It is tested on both simulated and in vivo human brain data. Evaluations show the improved reliability of the geometry information, reduced streaking artifacts, and increased accuracy of the susceptibilities of both basal ganglia and veins in the SCSWIM compared to other methods.