Metal-organic frameworks and its derivates have attracted much attention for energy storage application. In this work, three-dimensional bimetallic metal-organic frameworks with novel hierarchical bundle-like micro/nanostructure were synthesized at room temperature for the first time. After initial carbonization and subsequent selenization, hierarchical porous Ni-Co-Se nanoparticles embedded in 3D carbon network with a high surface area that obviously inherited the original morphology of the bimetallic metal organic frameworks. The resulting materials demonstrated superior performance as the anode in lithium ion batteries (LIBs): they provide high reversible Li-storage capacity, excellent cyclability (2061 mA h/g after 300 cycles) and high rate performance (493 mA h/g at 8 A/g). The features of Ni-Co-Se@C electrode include the synergistic effect of two metal selenides species for Li-storage, well-designed hierarchical porous bundle-like structure, steady carbon network and as-formed size-reduced particles after initial cycle process. These features not only enhanced the electronic properties and alleviated the volume variation of metal selenides during the repeated cycles, but also produced more active sites for lithium storage and a shorter lithium diffusion pathway to expedite the fast charge transfer and preserve a stable SEI layer, resulting in outstanding lithium storage performance. In addition, the pseudocapacitive behaviour contributes much to the high energy storage of lithium ions. These results uncover a facile methodology for the design of well-organized MOFs and transition metal dichalcogenides with 3D hierarchical structures.