The aggregation of Medin is closely associated with the arterial wall degeneration and cerebrovascular dysfunction. Medin aggregates are increased in cerebral arterioles of patients with vascular dementia or Alzheimer’s disease, and medin co-localizes with vascular amyloid-β (Aβ) deposits. Previous study demonstrated that Medin interacts directly with Aβ, forming heterologous fibrils with Aβ and promoting Aβ aggregation. However, the underlying mechanism of the co-aggregation between Medin and Aβ remains largely elusive. Here, we explored the interactions and conformational ensembles of Aβ₄₂/Medin trimers in different peptide environments (self-aggregation vs. co-aggregation) by performing allatom replica exchange molecular dynamic simulation on Aβ₄₂/Medin homotrimers and Aβ₄₂-Medin heterotrimer with an accumulated simulation time of 72 μs. Our results reveal that Aβ₄₂ exhibits higher affinity with Medin, and both Aβ₄₂ and Medin have similar molecular recognition sites for self-aggregation and co-aggregation. The N-terminus of Aβ₄₂ and the C-terminus of Medin play critical roles in Aβ₄₂-Medin cross-talk. More importantly, co-aggregation significantly alters the interaction strength, binding patterns and structural characteristics of Aβ₄₂ and Medin. Intermolecular interactions of Aβ₄₂ trimers are relatively weak among three trimers and the binding sites are concentrated between N- and N-termini, between N- and C-termini as well as between C- and C-termini of Aβ₄₂. In contrast, intermolecular interactions of Medin trimers are strongest and the binding sites are widely and uniformly distributed in Medin peptides. Intermolecular interactions of Aβ₄₂ in Aβ₄₂-Medin heterotrimer are decreased compared with Aβ₄₂ trimers, only the binding of the hydrophobic core regions (¹⁶KLVFFA²¹) is retained and other regions of Aβ₄₂ gain increased flexibility. 2D free energy landscapes reveal distinct conformational diversities among the homo- and heterotrimers, with the order of diversity being Medin/Aβ₄₂-Medin trimers > Aβ₄₂ trimers. The Rg of Aβ₄₂ trimers is smaller than that of the other two trimers, implying that Aβ₄₂ trimers adopt a more compact structure, whereas Medin/Aβ₄₂- Medin trimers exhibit a relatively loose conformation. Aβ₄₂ trimers possess the highest β content whereas Medin trimers exhibit the lowest β probability. We find that Aβ₄₂-Medin co-aggregation induces Medin to form more β-structures with longer length and fewer helices, while promotes Aβ₄₂ to form more helices and fewer β-structures. High β- propensity regions of Medin in heterotrimers shift towards the C-terminus of Medin, suggesting that Medin utilize its C-terminal β region as a core motif to drive its co-aggregation with Aβ₄₂. These results elucidate the detailed influences of co-aggregation on the interactions and conformations of Aβ₄₂ and Medin. This work provides key insights into the molecular mechanism of Aβ₄₂-Medin co-aggregation and the pathological cross-talk between related diseases.