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Located in the north margin of the Central Asian Orogenic Belt (CAOB), the early‐Permian Kalatongke Cu–Ni sulphide Orefield is the largest Cu–Ni ore deposit in Xinjiang province, NW China. After more than 30 years’ exploitation, the reserved resources of copper and nickel in the Kalatongke deposit is in serious shortage. The Cu–Ni deposits are characterized by ore‐bearing mafic rock, small‐size intrusion clusters, high copper content (Cu/Ni ratios approximately 3:2), high PGE content and a widespread massive sulphide lens. It consists of 13 small mafic intrusions, most of which are concealed underground. Although the ultramafic rock, which is the main host rock in most of the Cu–Ni deposits in the world, has not yet been found in these intrusions, it is still supposed to have a high content ultramafic rock at greater depths with a much better ore‐bearing potential. The mafic‐ultramafic intrusions have significant gravity and magnetic anomalies, which are carefully processed in this paper to present the 3D spatial distribution of concealed intrusions, indicating the magma source and upwelling direction for a better understanding of the formation of magmatic sulphide deposits in terms of magma conduit system. The residual gravity and magnetic anomalies originated by deep ultramafic intrusions are extracted by applying the matched filter, whose response functions are determined from the logarithmic power spectrum curves. Then the 2.5D joint gravity and magnetic modelling strategy was performed on five profiles to present interpretative sections for the concealed ultramafic intrusions with possible magma intrusion history. The density and magnetization model derived from the gravity and magnetic data inversion were useful constraints in constructing the initial model. The joint modelling results indicate that the concealed ultramafic intrusions are largest and deepest near profile C–C′ and become smaller and shallower towards northwest direction until vanish on profile A–A′. The intrusion centre of is likely to be located near profile CC′, north to the lower part of Y3. Magma then upwelling in two opposite directions (NW and SE) along faults F2, F3 and F6–8 to form shallower intrusions. The final 3D geological model illustrates the validity of the gravity and magnetic data in obtaining quantitative representations of the concealed ore‐bearing ultramafic intrusions and associated conduit system. Due to the full‐coverage and wide availability of gravity and magnetic data, the joint modelling results can provide useful guidance for better locating the deep ore‐bearing ultramafic intrusions in the exploitation of magmatic sulphide deposits, especially in areas with limited drilling data.