As an important part of organisms, proteins are of various types, and their functions and properties are different according to their structures. Therefore, it is of great significance to develop new uses of various proteins and their derivatives, increase the reuse value of protein-based biomass materials, and build a resource-saving and environment-friendly society. Protein-based separation membranes can be used to as environmentally friendly alternatives to conventional petroleum-based separation membrane materials. The separation membrane must have several beneficial properties, such as short transfer path lengths, low transfer resistances, high permeance and selectivity. In recent years, various forms of protein-based membranes with nanometer-scale thickness and unique membrane structures have been introduced to enable ultrafast and efficient separation. The rapid development of protein-based membranes has provided new avenues toward high flux separation membranes construction. In spite of their advantages and potential, there are major issues regarding the protein-based membrane that are not systematically addressed in the literature. In this paper, we conclude the representative potential applications of protein-based materials in membrane material science, providing emerging technologies and scrutinizing research and development challenges for membrane materials in this field. Finally, some important issues an perspectives for fundamental study and applications are briefly discussed.