The hierarchical assembly of inorganic and organic building blocks is an efficient strategy to produce high-performance materials which has been demonstrated in various biomaterials. Here, we report a layer-by-layer (LBL) assembly method to fabricate ultrathin hybrid films from nanometer-scale ionic clusters and proteins. Two types of cationic clusters (hydrolyzed aluminum clusters and zirconium-glycine clusters) were assembled with negatively charged bovine serum albumin (BSA) protein to form high-quality hybrid films, due to their strong electrostatic interactions and hydrogen bonding. The obtained hybrid films were characterized by scanning electron microscope (SEM), UV-vis, Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence (XRF), and X-ray diffraction (XRD). The results demonstrated that the cluster-protein hybrid films exhibited structural homogeneity, relative transparency, and bright blue fluorescence. More importantly, these hybrid films displayed up to a 70% increase in hardness and up to a 100% increase in reduced Young's modulus compared to the pure BSA film. These hybrid cluster-protein films could be potentially used as biomedical coatings in the future because of their good transparency and excellent mechanical properties.