Hydrogel system, as one of the most important biomaterials, is widely studied because of its tremendous potential in regenerative medicine conferred by its wide range of malleable biochemical and physical characteristics, which include its biocompatibility with the elemental biomolecules in vital tissues, its high water retention capability and adjustable soft-tissue-like physicochemical properties. These properties are modifiable to facilitate the targeted tissue protected from external damaging disturbance and having the encapsulated cells’ physiology-functional phenotypes induced or maintained in situ. Recently, hydrogels are increasingly used in the R&D of regenerative medicine to build complex tissue. Most of the insightful work focuses on how to select and fabricate the hydrogel models with desired physicochemical properties, flexibility of auto response to various bio-stimuli, and capability of efficiently forming the complex tissuemimicking construct at different scales. The present review introduced the major types of hydrogeis, the desirable physicochemical properties, the current fabrication methodologies and special organ-based cases of applications of hydrogels, which are used in complex tissue engineering. In addition, this review also discussed the major hurdles faced by the R&D of hydrogel systems for complex tissue medicine.