Here, we present microfluidic methods to fabricate complex hydrogel structures for 3D tissue or organ-like cell structures in vitro. First, a microfluidic system to continuously synthesize chemically and physically anisotropic Ca–alginate hydrogel microfibers is proposed to enable the guidance of cell proliferation and differentiation. Next, the microfluidic preparation methods for yarn-ball-shape hydrogel particles and extremely-small hydrogel microspheres. Finally, a newly developed micro-molding and bonding method for hydrogel micro-patterned plates is reported.