Silk fibroin (SF) is an excellent protein-based biomaterial produced by the degumming and purification of silk from cocoons of the Bombyx mori through alkali or enzymatic treatments. SF exhibits excellent biological properties, such as mechanical properties, biocompatibility, biodegradability, bioabsorbability, low immunogenicity, and tunability, making it a versatile material widely applied in biological fields, particularly in tissue engineering. In tissue engineering, SF is often fabricated into hydrogel form, with the advantages of added materials. SF hydrogels have mostly been studied for their use in tissue regeneration by enhancing cell activity at the tissue defect site or counteracting tissue-damage-related factors. This review focuses on SF hydrogels, firstly summarizing the fabrication and properties of SF and SF hydrogels and then detailing the regenerative effects of SF hydrogels as scaffolds in cartilage, bone, skin, cornea, teeth, and eardrum in recent years.