In the inverse problem, the traditional way to obtain a stable solution is based on the maximum smoothness criteria. However, this approach cannot generate clearer and more focused images. In this study, we propose an improved inversion method based on the smoothness constraints. In the algorithm, the model weighting functions are updated by adding a model’s total gradient module matrix, which can effectively constrain the boundary of the recovery model in the iterative operation. We invert the 3D magnetization intensity for the three-component magnetic data in the spatial domain by spherical coordinates. The preconditional conjugate gradient algorithm is introduced to improve the efficiency of the solutions. We design two sets of synthetic examples to evaluate the inversion effects, which show that the improved method is more reliable than the smoothness constraint method. The boundary of the magnetic bodies is more precise, and the magnetization ranges are more focused. The method does not rely on the initial model and is suitable for magnetic vector data inversion. We also apply the algorithm to a set of Dabie orogen three-component magnetic data derived from a geomagnetic field model and verify the effectiveness of the inversion method.