Nanofiltration membranes with controlled pores are useful in many fields, such as pharmaceuticals, desalination, petroleum, and food processing. Recently, graphene oxide has emerged as a promising candidate for the fabrication of highly efficient and pressure-resistant nanofiltration membranes with excellent water permeability and solute rejection. However, it remains difficult to achieve increased permeability while maintaining excellent separation ability. Herein, we report a novel silk fibroin-graphene oxide (FGO) composite membrane prepared by using fibroin as a cross-link reagent, which is extracted from natural Bombyx mori silkworm cocoons. Such a FGO membrane shows a pure water permeance of ∼280 L m−2 h−1 bar−1, which is five times greater than previously reported GO-based membranes. Further, such a membrane also exhibits excellent separation efficiency (> 99 %) for different feed molecules. Additionally, these membranes exhibit high chemical stability in water, acidic and basic solutions for several days compared to pristine GO membranes.