<p>The Bangong-Nujiang Suture Zone (BNSZ) is an important geological tectonic belt in the Qinghai-Tibet Plateau. Although previous studies have conducted extensive integrated research on this suture belt, there is still significant controversy regarding its deep geological structure, fault systems, and the distribution of magmatic rocks due to limitations imposed by conventional geological survey methods. By employing the latest large-scale, high-precision airborne gravity and magnetic data, this study utilized potential field transformation methods to systematically analyze the gravity and magnetic field characteristics of the middle segment of the BNSZ and its adjacent areas. The results reveal that the suture zone exhibits a large-scale, belt-shaped gravity and magnetic anomaly feature, which significantly differs from the anomaly characteristics observed in adjacent tectonic units. Based on these distinct anomaly features, this study redefines the spatial position of the northern boundary fault of the suture zone and proposes that the Nima segment of the northern boundary fault should be shifted 30–45 km southward from its previously interpreted location. By integrating rock physical property data, the spatial distribution of concealed magmatic rocks within the suture zone has been further delineated. Inversion results show that intermediate-acidic and ultramafic rocks are extensively developed within the zone, and their distribution is clearly fault-controlled. To reconstruct the deep geological structure, a joint gravity-magnetic inversion technique was applied to develop a deep crustal model. The results indicate significant uplift within the suture zone, with a depth difference of 2–3 km compared to the basement of adjacent areas. This study provides important geophysical evidence for investigating deep processes and mineral exploration potential in the middle segment of the BNSZ, while also offering new insights into the geodynamic processes of the tectonic evolution of the Qinghai-Tibet Plateau.</p>