AbstractNanocomposites made from alginate and nanoclay are extensively applied for diverse biomedical applications. However, the lack of a clear understanding of the interactions between alginate and nanoclay makes it difficult to rationally design the nanocomposites for different material extrusion‐based 3D bioprinting strategies. Here, a combined analytical model is proposed to accurately predict the interaction mechanisms between alginate and nanoclay through small‐angle neutron scattering. These mechanisms are summarized into a phase diagram that can guide the design of alginate‐nanoclay nanocomposites for different bioprinting applications. The rheological properties of various nanocomposites are measured to validate the proposed interaction mechanisms at the macroscale. Accordingly, three representative extrusion‐based bioprinting strategies are linked with the nanocomposite design and applied to freeform fabricate complex structures. A roadmap is summarized to bridge the gap between biomaterial design and bioprinting processes, enabling the rapid and rational selection of biomaterial formula based on available 3D printing methods, and vice versa.