Here, we report a general and facile method for effective layer-by-layer exfoliation of transition metal dichalcogenides (TMDs) and graphite in water by using protein, bovine serum albumin (BSA) to produce single-layer nanosheets, which cannot be achieved using other commonly used bio- and synthetic polymers. Besides serving as an effective exfoliating agent, BSA can also function as a strong stabilizing agent against reaggregation of single-layer nanosheets for greatly improving their biocompatibility in biomedical applications. With significantly increased surface area, single-layer MoS2 nanosheets also exhibit a much higher binding capacity to pesticides and a much larger specific capacitance. The protein exfoliation process is carefully investigated with various control experiments and density functional theory simulations. It is interesting to find that the nonpolar groups of protein can firmly bind to TMD layers or graphene to expose polar groups in water, facilitating the effective exfoliation of single-layer nanosheets in aqueous solution. The present work will enable to optimize the fabrication of various 2D materials at high yield and large scale, and bring more opportunities to investigate the unique properties of 2D materials and exploit their novel applications.