Current approaches to design monodisperse protein assemblies require rigid, tight, and symmetric interactions between oligomeric protein units. Here, we introduce a new multivalent interaction‐driven assembly strategy that allows flexible, spaced, and asymmetric assembly between protein oligomers. We discovered that two polygonal protein oligomers (ranging from triangle to hexagon) dominantly form a discrete and stable two‐layered protein prism nanostructure via multivalent interactions between fused binding pairs. We demonstrated that protein nano‐prisms with long flexible peptide linkers (over 80 residues) between protein oligomer layers could be discretely formed. Oligomers with different structures could also be monodispersely assembled into two‐layered but asymmetric protein nano‐prisms. Furthermore, producing higher‐order architectures with multiple oligomer layers, for example, 3‐layered nano‐prisms or nanotubes, was also feasible.