In order to develop superhydrophobic and self-cleaning materials based on biomass, a simple and moderate method was used herein to grow Cu3(PO4)2·3H2O nanoflowers on the surface of soy protein isolate (SPI) film. Relying on the controllably hierarchical micro/nano-structures of the nanoflowers, the wetting behavior of resultant film can be tuned. The stability of the nanoflowers on an SPI surface was excellent because of the coordination interaction between SPI and copper ions. In particular, the superhydrophobic surface can resist moderate acid and base without losing the antiwetting property. Furthermore, a self-cleaning function was achieved for the SPI film fully covered with the nanoflowers. Such biobased film will be of great interest to biomedical and industrial applications.