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Abstract Despite recent progress, it remains challenging to program biomacromolecules to assemble into discrete nanostructures with pre‐determined sizes and topologies. We report here a novel strategy to address this challenge. By using two orthogonal pairs of heterodimeric coiled coils as the building blocks, we constructed six discrete supramolecular assemblies, each composed of a prescribed number of coiled coil components. Within these assemblies, different coiled coils were connected via end‐to‐side covalent linkages strategically pre‐installed between the non‐complementary pairs. The overall topological features of two highly complex assemblies, a “barbell” and a “quadrilateral” form, were characterized experimentally and were in good agreement to the designs. This work expands the design paradigms for peptide‐based discrete supramolecular assemblies and will provide a route for de novo fabrication of functional protein materials.