Nanometric topological spin textures, such as magnetic skyrmions (Sks) and antiskyrmions (antiSks), have attracted much attention in condensed matter physics and spintronics. To date, most studies have focused on two-dimensional Sks and antiSks in thin films with inherent or synthetic antisymmetric spin exchange interaction, termed Dzyaloshinskii–Moriya interaction, for their topological features and information-carrier functions. Although three-dimensional (3D) spin textures are ubiquitous, previous studies have focused mostly on cylindrical Sks or other non-topological magnetic vortices. Nontrivial 3D spin textures, such as antiSks composed of alternating Bloch- and Néel-type spin spirals, chiral bobbers carrying emergent magnetic monopoles, and deformed Sk strings, have rarely been identified, particularly on their topological nature. To elucidate these textures, we have developed a 3D nanometric magnetic imaging technique - tomographic Lorentz transmission electron microscopy. This approach enables not only the visualisation of 3D shape of magnetic objects, but also their 3D vector field mapping. The present research will lead to discoveries and advanced understanding of fertile 3D magnetic structures in a broad class of magnets, providing insight into 3D topological magnetism.