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The use of natural protein-based thin films has been severely limited due to their relatively low stiffness and strength compared to synthetic polymers. Although the mechanical properties of the protein-based thin films could be enhanced through blending with nanofillers, the fabrication of these materials with nanoscale-to-macroscale hierarchical architecture and robust interfacial adhesion via a facile and green method remains a challenge. Here we prepared robust protein-based organic/inorganic nanocomposite films with a nacre-like microstructure through directly regulating protein conformation in a simple and biocompatible all-aqueous system. These films contain a high concentration of Laponite (Lap) and amyloid-like phase-transited bovine serum albumin (PTB) aggregates rich in β-sheets which could organize Lap nanoplatelets into an intercalated and multistacked structure. In addition, the PTB aggregates present strong mechanical strength, good stability and especially superior bioadhesion to afford strong organic/inorganic interface bonding. The resultant PTB/Lap films exhibit high Young’s modulus and strength, good chemical stability (in both aqueous solution and organic solvent) and flame retardation, while they are also very transparent (maintaining more than 90% transmittance). Moreover, the film could adhere onto various substrates with robust biomimetic interfacial adhesion, and the resultant coating on glass could function as a smart window to cool down the indoor temperature. Because of their excellent performance and high versatility, the amyloid-like protein/clay nanocomposite films are expected to find broad practical applications.