We study the inversion of magnetic data acquired over a rugged observation surface and where the buried source bodies have strong remanent magnetization that leads to unknown total magnetization directions. These factors pose significant challenges for processing and inversion of such data. To tackle the challenges from both a rugged observation surface and an unknown magnetization direction, we propose a strategy through the joint use of the equivalent source technique and 3D amplitude inversion to obtain 3D magnetization strength. We use equivalent source processing to calculate the amplitude data in the space domain because the use of the wavenumber-domain method is invalid due to large variations in the data elevation. We then carried out an amplitude inversion to generate a 3D subsurface distribution of the magnitude of the total magnetization vector. The results from a synthetic example and aeromagnetic data in Daye Mine in China showed that this approach is effective and images the magnetic units whose contact zones with the limestone country rock host the mineralization. The method is general and can be applied to a variety of cases with similar challenges.