ABSTRACT: Epidemiological studies have shown that the development of Alzheimer’s disease (AD) is associated with type 2 diabetes (T2D), but it still remains unclear how AD and T2D are connected. Heterologous cross-seeding between the causative peptides of Ab and hIAPP may represent a molecular link between AD and T2D. Here, we computationally modeled and simulated a series of cross-seeding double-layer assemblies formed by Ab and hIAPP peptides using all-atom and coarse-gained molecular dynamics (MD) simulations. The cross-seeding Ab–hIAPP assemblies showed a wide range of polymorphic structures via a combination of four b-sheet-to-b-sheet interfaces and two packing orientations, focusing on a comparison of different matches of b-sheet layers. Two cross-seeding Ab–hIAPP assemblies with different interfacial b-sheet packings exhibited high structural stability and favorable interfacial interactions in both oligomeric and fibrillar states. Both Ab–hIAPP assemblies displayed interfacial dehydration to different extents, which in turn promoted Ab–hIAPP association depending on interfacial polarity and geometry. Furthermore, computational mutagenesis studies revealed that disruption of interfacial salt bridges largely disfavor the b-sheet-to-b-sheet association, highlighting the importance of salt bridges in the formation of cross-seeding assemblies. This work provides atomic-level information on the cross-seeding interactions between Ab and hIAPP, which may be involved in the interplay between these two disorders.