In this study, we developed a procedure for assembling hepatic microstructures into tube shapes using magnetic self-assembly for in vitro 3D micro-tissue fabrication. To this end, biocompatible hydrogels, which have a toroidal shape, were made using the micro-patterned electrodeposition method. Ferrite particles were used to coat the fabricated toroidal hydrogel microcapsules using a poly-L-lysine membrane. The microcapsules were then magnetized with a 3 T magnetic field, and assembled using a magnetic self-assembly process. During electrodeposition, hepatic cells were trapped inside the microcapsules, and they were cultured to construct tissue-like structures. The magnetized toroidal microstructures then automatically assembled to form tube structures. Shaking was used to enhance the assembly process, and the shaking speed was experimentally optimized to achieve the high-speed assembly of longer tube structures. The flow velocity inside the dish during shaking was measured by particle image velocimetry. Hepatic functions were evaluated to check for side-effects of the magnetized ferrite particles on the microstructures. Collectively, our findings indicated that the developed method can achieve the high-speed assembly of a large number of microstructures to form tissue-like hepatic structures.