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Binary transition metal selenides (BTMSs) are more promising than single transition metal selenides (TMS) as anode materials of sodium-ion batteries (SIBs). However, it is still very challenging to prepare high-performance BTMSs in the pure phase, instead of a mixture of two TMSs. In this study, a binary metal center-based MOF derived selenization strategy was developed to prepare iron–cobalt selenide (Fe2CoSe4@NC) and iron–nickel selenide (Fe2NiSe4@NC) nanocomposites in the single phase and when wrapped with carbon layers. As the anode material of SIBs, Fe2CoSe4@NC exhibits higher long-term cycling performance than Fe2NiSe4@NC, maintaining a capacity of 352 mAh g−1 after 2100 cycles at 1.0 A g−1, which is ascribed to the higher percentage of the nanopores, larger lattice spacing, and faster Na+ diffusion rate in the electrode materials of the former rather than the latter.