In the biomedical micro-electromechanical systems (MEMS) field, the fabrication of three-dimensional (3D) magnetic hydrogel microdevices and microactuators with sizes smaller than 100 mu m is difficult. In this paper, magnetic-field-driven 3D hydrogel microstructures were fabricated through four steps: the synthesis of surface-modified Fe3O4 nanoparticles (Fe3O4 NPs), the preparation of a magnetic gel photoresist, two-photon polymerization microfabrication, and a solvent-exchange process. For the preparation of a stable magnetic gel photoresist, surface-modified Fe3O4 NPs with an average size of 7.8 nm were synthetized and well dispersed in gel photoresist. The magnetic gel photoresist exhibited a good UV photopolymerization effect, and a magnetic-field-driven macroscopic hydrogel was prepared. The two-photon polymerization properties of gel photoresists with various Fe3O4 NP contents were investigated in detail, and the minimum width of fabricated lines reached 106 nm for the photoresist with 0.32 wt% Fe3O4 NPs. Three hydrogel microstructures-the Qingdao University logo, a magnetically actuated micro-rod, and a magnetically actuated micro-nail-were successfully fabricated using a gel photoresist with 0.96 wt% Fe3O4 NPs. Importantly, obvious and reversible external-magnetic-field-driven bending behavior of the 3D hydrogel micro-nail with a size of 10 mu m was observed.