Three-dimensional (3D) structural analysis is an important field in physical and biological sciences. There exist two groups of electron microscopy methods that are capable of providing 3D structural information of an object, i.e., electron tomography and depth sectioning. Electron tomography is capable of resolving atoms in all three dimensions, but the accuracy in atomic positions is low and the object size that can be reconstructed is limited. Depth sectioning methods give high positional accuracy in the imaging plane, but the spatial resolution in the third dimension is low. In this work, electron tomography and depth sectioning are combined to form a method called multiple-section local-orbital tomography, or nLOT in short. The nLOT method provides high spatial resolution and high positional accuracy in all three dimensions. The object size that can be reconstructed is extended to a million atoms. The present method establishes a foundation for the widespread application of atomic electron tomography.