A tool for problem of inversion of geopotential fields has been developed for GIS INTEGRO under the name of “assembly method”, a family of which is currently gaining attention. In the article the capabilities of this specific implementation are being examined in the application to inversion of magnetic fields for regional 3D-modelling of large oil and gas perspective territories. The available methods of control and regularization of minimization of field residual are investigated using synthetic model data in the application to magnetic data and their differences to more well-understood gravity fields. In particular, a value of “depth priority” has the similar effect on model evolution as in the case of gravity problem, but the balanced value is larger. In the last section, an example of the method application is presented: the parameters of lithospheric source of satellite magnetic anomaly associated with Guli massif are investigated.