Qiongheba is a polymetallic ore concentration area located in the east margin of the Junggar Basin in Xinjiang, Northwest China. Because all three main types of metal deposits (porphyry-type copper, skarn-type iron-copper, and structural altered rock-type gold deposits) in this area are controlled strictly by fault structures and intrusions buried under the Quaternary sediments, the detection of concealed faults and intrusions is of great significance for mineral prospecting. We aim to make clear the faults and intrusions based on the high-precision gravity and magnetic data set. First, multiscale edge detection of gravity and magnetic data is used to distinguish and divide the faults system. Second, 3D recognition of concealed intrusions combining with 3D inversion and multiscale edge detection of gravity and magnetic is carried out to construct the 3D formation of concealed intrusions. Last, seven prospecting targets are proposed based on our research and existed regional geologic and geochemical information, and two of them have been confirmed to be rich in polymetal (Cu-Fe-Mo-Au in the Layikeleke deposit and Cu in the Baxi deposit) by drilling. Our research results not only proved the effectiveness of the combination method of 3D inversion and multiscale edge detection of gravity and magnetic data in the prospecting of concealed faults and intrusions, but they also provide abundant information for mineral exploration prediction in the Qiongheba area.