Over the past decade, the hydrogels prepared from silk fibroin have received immense research attention due to the advantages of safe nature, biocompatibility, controllable degradation and capability to combine with other materials. They have broad application prospects in biomedicine and other fields. However, the traditional silk protein hydrogels have a simple network structure and single functionality, thus, leading to poor adaptability towards complex application environments. As a result, the application fields and development have been significantly restricted. However, the development of functional silk protein hydrogels has provided the opportunities to overcome the limitations of the silk protein hydrogels. In recent years, the functional design of the silk protein hydrogels and their potential applications have attracted the attention of scholars worldwide. Nevertheless, a comprehensive review on functional silk protein hydrogels is missing so far. In order to gain an in-depth understanding of the development status of the functional silk protein hydrogels, this article reviews the current status of the preparation, properties and application of the functional silk protein hydrogels. The article first briefly introduces the current cross-linking methods (including physical and chemical cross-linking), principles, advantages and limitations of the silk protein hydrogels. Subsequently, the types of functional silk protein hydrogels (e.g., high strength, injectable, self-healing, adhesive, conductive, environmental stimuli-responsive, 3D printable, etc.) and design principles for functional implementation have been introduced. Next, based on the advantages of the various functional aspects of the silk protein hydrogels, the applications of these hydrogels in the biomedical field (tissue engineering, sustained drug release, wound repair, adhesives, etc.) and bioelectronics are reviewed. Finally, the development prospects and challenges associated with silk protein functional hydrogels have been analyzed. It is hoped that this study will contribute towards the future innovation of the silk protein hydrogels by promoting the rational design of new mechanisms and successful realization of the target applications.