Protein-based hydrogels are promising materials for tissue engineering and drug delivery due to the unique properties of proteins such as perfect polydispersity, exact control over monomer sequence, ability to fine-tune molecular-level biochemical interactions, etc. This tutorial review summarizes recent progress on the preparation of protein-based hydrogels and their applications. Typically, we introduce two strategies of covalent and non-covalent ones for the preparation of hydrogels. Hydrogels prepared by the covalent strategy are stable and can respond to the conformational change of proteins. They can be applied for cells encapsulation, screening of drug molecules and heavy metals, etc. Hydrogels formed by non-covalent interactions are injectable physical hydrogels. The simple mixing preparation strategy and fast gelation kinetics guarantee the homogeneous encapsulation of cells and therapeutic agents within them. Therefore, they have been widely applied for the delivery of bioactive components, regenerative medicine, etc. The challenges that remained in this field are also summarized in this paper. We envision that rationally designed protein-based hydrogels will have broad applications in many areas including controlled delivery, tissue engineering, drug screening, etc.