The aim of this study is 3D inversion of magnetic anomalies at the area of Janja copper deposit in Sistan and Baluchestan province, whereby alteration zones associated with the mineralization based on the magnetic susceptibility model are determined. According to Li- Oldenburg nonlinear algorithm, modeling of geological structures with complex geometric distribution can be done with high accuracy. By assigning magnetic susceptibility to each cell, the three-dimensional shape of the underground body that produces the magnetic anomaly can be reconstructed. The anomalous areas are a good approximation of the potential sites of potassic and propylitic alterations, on which exploratory drilling can be more easily located. The research result in the investigated area indicates a relatively large source with a depth of 50 m to 170 m.