Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and electron probe X-ray microanalysis (EPMA) have been employed to determine major and trace elemental concentrations in magnetite from different ores in the Laoshankou deposit, which is the most important Fe-Cu-Au deposit in the northern margin of East Junggar. Two magnetite-associated paragenetic sequences have been defined in Laoshankou, including amphibole-epidote-magnetite alteration/mineralization (stage II) and pyrite-chalcopyrite mineralization (stage III-B). On the basis of the magnetite textures and chemical compositions, we have identified six generations of magnetite from three types of ores/rocks, including the high-Ti inclusion-rich M-1-A and inclusion-free M-1-B in massive magnetite-epidote-amphibole ores (type H1) from stage II; the low-Ti, high-Si, inclusion-rich M-1-C in massive magnetite-sulfide ores (type H2) from stage II; the ubiquitous low-Ti M-2 and pristine low-Ti, low-Si M-3 in both H1 and H2 types; and M-4 within massive chalcopyrite-magnetite ores (type H3) from stage III-B. The discriminations of V versus Ti, Ca + Mn + Al versus Ti + V, and Fe versus V/Ti, as well as mineral assemblages and trace element concentrations of Cr (<1000 ppm) and V (<300 ppm), collectively imply that all the generations of magnetite are hydrothermal in origin, and more likely similar to those in iron-oxide copper-gold deposits. The diverse textural and chemical features among these generations of magnetite indicate that they have formed from distinct process. The earliest M-1-A and M-1-B in type H1 ore and M-1-C in type H2 ore were replaced by M-2 along fractures and/or grain boundaries of the M-1-A/B/C, forming a number of mineral inclusions via dissolution and reprecipitation. Following this, M-3 veins generally crosscut all of these above types. Finally, high-Co, Ni, and REE-rich fluid formed the chalcopyrite-associated M-4 with dark-light zoning in the type H3 ore from pyrite-chalcopyrite mineralization. These elevated lithophile (REE) and chalcophile (Co, Ni) elements within the chalcopyrite (sulfide)-associated M-4 further suggest that non-magmatic fluid dominated in the fluid system, with intensive fluid-rock interactions and low-temperature, Cl, and Cu-rich external fluid accounting for the Cu-Au mineralization.