Transition metal sulfides (TMSs) with high theoretical capacity and outstanding electrochemical activity has been recognized as promising sodium ion (Na+) storage electrodes. However, conventional TMSs electrodes often exhibit low adsorption capacity and cycling performance, primarily attributed to low loading and significant volume expansion during cycling. Herein a “microbial self-driven” strategy is proposed to synthesize highly loaded ZnS-Ni3S2 heterostructure composites (ZnS-Ni3S2@NB). Ultra-long and ultra-thin Aspergillus niger nanoribbons in ZnS-Ni3S2@NB form interlaced conductive networks, which accelerate the rapid movement of electrons. The highly loaded ZnS-Ni3S2 heterostructures were highly dispersed and uniformly anchored, exposing abundant active sites while enhancing the pseudocapacitance and thus the Na+ adsorption performance. Moreover, the carbon skeleton formed by nanoribbons enhanced the structural stability of the electrode and provided space to slow down the volume expansion of ZnS-Ni3S2. Consequently, the electrode demonstrates exceptional Na+ storage capacity (45.7 ± 2.14 mg g−1 at 50 mA g−1) and excellent cycling stability. Futhermore, density-functional theory calculations (DFT) elucidate the electric double layer (EDL) and pseudocapacitance mechanisms, while finite element simulations confirm the advantages of the highly loaded ZnS-Ni3S2 heterojunction composite structure in mitigating stress concentration and volume expansion. This work provides a novel strategy to utilize microbial self-driven construction of heterointerfaces to enhance the storage capacity and cycling stability of TMSs.