In the volcanically and tectonically active zones of the main Ethiopian Rift, geothermal resources are primarily influenced by subsurface geological structures along the rift valley floor which contains multiple volcanic complexes. However, the specific subsurface structures of these volcanic systems and their relation to the distribution of shallow geothermal resources remain inadequately understood. This study utilizes gravity data from the Global Gravity Model Plus2013 and ground magnetic data to investigate the role of subsurface volcanic features in the occurrence of geothermal resources within the Boku Geothermal Prospect (BGP). Interpretation of gravity and magnetic anomalies, along with derivative maps, suggests the presence of a potential geothermal heat source beneath the Boku geothermal area. The 2D joint gravity and magnetic models, combined with gravity and magnetic anomalies, indicate a dense mafic intrusion at approximately 4.5 km depth beneath the BGP, which is likely the heat source for the geothermal system. Linear features (trending NNE-SSW and NE-SW), interpreted as faults and weak zones from derivative maps, appear to play a crucial role in hydrothermal circulation by acting as conduits for transporting hydrothermal fluids, facilitated by these faults and weak zones. Our 2D models reveal interactions between Quaternary faults within the Wonji Fault Belt (WFB) and the subsurface mafic intrusion, elucidating the mechanism by which thermal heat is transported to the shallow subsurface and surface. The surface thermal manifestations are strongly correlated with the structures detected by Horizontal Derivative and Analytic Signal analyses, indicating that the BGP area is structurally controlled. This complex faulting system provides extensive permeability and favorable conditions for the occurrence of geothermal resources within the BGP.