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The data presented in this article are related to “Odd-even phonon transport effects in strained carbon atomic chains bridging graphene nanoribbon electrodes” (Kim et al., 2019). To provide the information that can be utilized in reproducing our results, we provide the fully optimized graphene nanoribbon (GNR)–carbon chain (CC)–GNR junction atomic configurations at different strain values, the computational setting for quantum phonon transport calculations, and several computational data that were not included in the main manuscript. Data on graphene–CC–graphene junctions are additionally presented.