Many soft tissues of the human body possess hierarchically anisotropic structures, exhibiting orientation-specific mechanical properties and biological functionality. Hydrogels have been proposed as promising scaffold materials for tissue engineering applications due to their water-rich composition, excellent biocompatibility, and tunable physico-chemical properties. However, conventional hydrogels with homogeneous structures often exhibit isotropic properties that differ from those of biological tissues, limiting their further application. Recently, magnetically anisotropic hydrogels containing long-range ordered magneto-structures have attracted widespread interest owing to their highly controllable assembly strategy, rapid magnetic responsiveness and remote spatiotemporal regulation. In this review, we summarize the latest progress of magnetically anisotropic hydrogels for tissue engineering. The fabrication strategy of magnetically anisotropic hydrogels from magnetic nanofillers with different dimensions is systemically introduced. Then, the effects of magnetically anisotropic cues on the physicochemical properties of hydrogels and the cellular biological behavior are discussed. And the applications of magnetically anisotropic hydrogels in the engineering of different tissues are emphasized. Finally, the current challenges and the future perspectives for magnetically anisotropic hydrogels are presented.