Laser powder bed fusion method is popularly applied in the additive manufacturing of metal parts. The void defect and microstructure are the main factors which determine their mechanical properties. However, the characterization of microstructure and cavities is two dimensional, which is hard to show the spatial profile. In this paper, in order to explore the microstructure and defects in three dimensions, the combined continuously slicing and microstructure observation was used to investigate the microstructure of an Inconel 718 sample. The sample was sliced 468 layers with thickness of 1 µm by xenon ion beam, a 142.8 µm* 107 µm* 46.8 µm microstructure cube was reconstructed. From the 3D model, the melt pool, cavity, pore and grains and their orientations were analyzed. The results provide spatial features of its microstructure. The equi-axed grains are among the coarse column grains, and some are the original grains of insufficiently melt or totally unmelt powder particles. The results tell the difference of the two kinds of voids, i.e., cavity and pore.