It requires excellent conductivity, rapid diffusion of electrolyte and high active specific area of active materials to achieve efficient supercapacitor. Herein, the novel NiCo2S4-Ni9S8-C double-layered yolk-shell microspheres (NiCo2S4Ni9S8-C DYMs) were synthesized by using bimetallic metal-organic framework (MOF) as self-template. The microspheres are composed of numerous tiny heterogeneous NiCo2S4-Ni9S8 nanoparticles (similar to 10 nm in size) decorated in amorphous carbon. As expected, the sample exhibits high specific capacity of 293.6 mAh g(-1) at 1 A g(-1), excellent rate capacity (81.1% from 1 A g(-1) to 20 A g(-1)) and good cycling stability (capacity retention of 87.3% over 5000 cycles). The hybrid supercapacitor assembled by NiCo2S4-Ni9S8-C DYMs and grapheme hydrogel, shows an energy density of 51 Wh kg(-1) at a power density of 1399.4 W kg(-1) and even can retain 32.5 Wh kg(-1) at 8004.4 W kg(-1). The density functional theory (DFT) calculation show the hetero-interfaces of NiCo2S4-Ni9S8 can optimize the electronic distribution, coupled with the excellent electroconductivity of dispersed carbon within microspheres, which boost the electrochemical performance. This work provides an approach to fabricate heterogeneous microspheres by MOF route for developing advanced battery-type electrode materials.