In this paper, we propose new variational model for image registration from tomographic data. First, we employ the topological gradient approach for a tomographic reconstruction that uses the first‐ and the second‐order discontinuities in order to detect important objects of a given observed X‐ray tomographic data (sinograms). Second, we use this geometric information furnished by a high‐order operator in order to define an appropriate fidelity measure for the image registration process. A theoretical study of the proposed model is provided; Gauss–Newton method and multilevel technique are used for its numerical implementation. The performed numerical experiments show the efficiency and effectiveness of our model.