Water-soluble Cu nanoclusters (NCs) and Zn NCs capped with a vegetable protein, soy protein isolate (SPI), are designed and synthesized for regulation of the rigidity and flexibility of bio-films. The special bio-films from SPI modified by Cu NCs exhibit better mechanical property, and those modified with Zn NCs show better hydrophobic property. UV-vis absorption spectroscopy demonstrated that Cu NCs and Zn NCs have formed, and Fourier transform infrared spectroscopy revealed that there was no change in the basic structure of the protein, but the SPI molecule chains and functional groups might be influenced, which made the cross-linking density increase. X-ray photoelectron spectroscopy suggested Cu and Zn were in the zero-valent state. X-ray diffraction patterns of SPI films indicated that metal nanoclusters changed the conformation of SPI from compact to unfolded. Water vapor permeability, oxygen permeability and nitrogen permeability of these metal nanocluster-modified films have been improved, and these films are proven safe enough to be used in contact with food.