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The application of silicon-based anode remains a serious challenge due to its intrinsic volumetric expansion effect and low conductivity. In our work, a novel CNT-interspersed hierarchical carbon shell structure (denoted as PDA@CoZn-NC@Si) is synthesized by wrapping Si uniformly in the bimetallic zeolite imidazolate frameworks (ZIFs) and then encapsulated with a dopamine-derived carbon shell. The PDA@CoZn-NC@Si anode delivers better cycle stability of 814 mAh/g at 0.5C for 400 cycles (only −0.14% capacity reduction per cycle) and possesses excellent rate capability, which benefits from the inner porous buffer spaces, interspersed CNT, and solid heterogeneous carbon shells. In addition, the full cell is assembled by pairing a solution-based chemically prelithiated PDA@CoZn-NC@Si anode with a Li(Ni1/3Co1/3Mn1/3)O2 (NCM111) cathode, and it presents an improved initial coulombic efficiency (88.3%) and a high energy density (419.8 Wh/kg). This study provides effective guidance for optimizing the microstructure design and prelithium of Si-based anodes.