In this study, we report the microfluidic-based synthesis of a multifunctional Janus hydrogel particle with anisotropic superparamagnetic properties and chemical composition for the bottom-up assembly of hydrogel superstructures. In a uniform magnetic field, the resulting Janus magnetic particles fabricated in the present method exhibit chainlike or meshlike superstructure forms, the complexity of which can be simply modulated by particle density and composition. This controllable field-driven assembly of the particles can be potentially used as building blocks to construct targeted superstructures for tissue engineering. More importantly, we demonstrated that this method also shows the ability to generate multifunctional Janus particles with great design flexibilities: (a) direct encapsulation and precise spatial distribution of biological substance and (b) selective surface functionalization in a particle. Although these monodisperse particles find immediate use in tissue engineering, their ability to self-assemble with tunable anisotropic configurations makes them an intriguing material for several exciting areas of research such as photonic crystals, novel microelectronic architecture, and sensing.