Non-uniqueness is a problem encountered while imaging subsurface susceptibility by inverting magnetic field surveys. We propose a novel method to construct velocity-susceptibility initial models using Vp together with the Vp/Vs ratio from seismic tomography to improve the model which satisfies more information and better identifies locations of high-susceptibility materials. For comparison, two recovered susceptibility structures are derived from two distinct initials (homogeneous and velocity-susceptibility) models through the standard inversion process. Two profiles with intense undulation of magnetic anomalies over sedimentary areas in central-west Taiwan and complex geological structures at the rim of the subduction zone in northeast Taiwan are used as examples to compare the results of the initial models. The inversion results suggest that the susceptibility structures from both models agree in terms of the location of the fault zones, specifically at depth < 10 km. Recovered susceptibility structures derived from the velocity-susceptibility initial model agree with the geological structure that reduces uncertainty at depth > 10 km. Consequently, the initial model with velocity constraints lowers the non-uniqueness associated with the inversion of magnetic anomalies.