Strong hydrothermal alteration modifies rock physical properties in iron oxide-copper-gold deposits (IOCGs) and may result in characteristic signatures detectable in geophysical surveys. Magnetic data are commonly used in characterizing orebodies, and 3D inversions are often used to assist in interpretations. In areas with strong remanence and self-demagnetization, the total magnetization can have directions different from the inducing field direction. This deviation precludes the use of traditional inversion methods. Magnetic amplitude inversion offers one solution to this challenge because the amplitude data are weakly dependent on the magnetization direction. In addition, the low magnetic latitude also imposes difficulty in amplitude data calculation due to the instability in the component conversion in the wavenumber domain. To formulate a practical approach, we present a case study on applying the magnetic amplitude inversion to the Furnas southeast IOCG deposit at the low magnetic latitude in Carajás Mineral Province, Brazil, and demonstrate that the approach can reliably recover an interpretable distribution of effective magnetic susceptibility and identify massive magnetite from hydrothermal alterations associated with the high-grade ore.