Three-dimensional reconstruction of atomic structure, known as atomic electron tomography (AET), has found increasing applications in materials science. The AET has been limited to very small nanoparticles due to the challenges of obtaining accurate atomic positions for large objects, for which the projection approximation generally assumed in AET is no longer valid due to the evolution of the electron probe along the beam direction. To address these challenges, we have developed a method that represents atoms as local orbitals and implements a depth-dependent probe-object interaction. Compared to conventional tomographic methods, the accuracy of atomic positions is improved by a factor of three and provides a solution for the tomographic reconstruction of large objects.