Abstract: With the gradual depletion of shallow and easily discoverable mineral deposits in China, making mineral exploration a critical issue to be addressed urgently. The East Tianshan–Beishan orogenic belt, as an important component of the central segment of the southern margin of the Central Asian Orogenic Belt, serves as a key base for strategic mineral resources such as copper, nickel, and cobalt. Although significant progress has been made in the study of metallogenic belts in this region, their extent and scale remain highly uncertain. To reassess the distribution and key structural attributes of deep-seated faults in the area, this study employed the normalized vertical derivative of the total horizontal derivative of gravity anomaly (NVDR-THDR) method to identify the planar distribution of these faults. Combined with residual Bouguer gravity anomaly and integrated gravity-magnetic data, we propose that the Kanggur Fault Zone should be regarded as a plate-boundary fault rather than a secondary fault along the northern margin of the suture zone. Meanwhile, the Yamansu Fault Zone is interpreted as a secondary fault within the Kanggur suture zone, rather than a relic of an ancient plate boundary or a product of intracontinental deformation. In terms of metallogenic information extraction, the minimum curvature method for potential field separation was applied for the first time to geochemical data to extract ore-forming anomaly characteristics. Additionally, the ACE (Alternating Conditional Expectations) regression algorithm was used to integrate gravity, magnetic, and Cu-Ni-Co metallogenic anomaly features. By integrating known Cu-Ni ore occurrences, the distribution of deep-seated faults, and multi-source data fusion results, two prospective metallogenic belts (the Yamansu Fault Belt and the Xingxingxia Fault Belt) were identified, and six favorable ore-forming target areas were delineated. The findings of this study provide a scientific geophysical basis for tectonic unit division and mineral resource exploration in the East Tianshan–Beishan region.