This paper presents the formation of complex cross-sectional microfibers using three-dimensional microfluidic devices. The compartments and shapes of core and shell layers in the microfibers were independently controlled via three-dimensional fluidic channels fabricated by the combination of sheath units. The number of layers is easily expanded by the stacking of these units. Therefore, the highly heterogeneous microfibers of alginate hydrogel are obtained in polydimethylsiloxane structures. This widely expandable method has great potential for the development of functional and complex fiber-shaped materials.