Transition metal chalcogenides (TMCs) with high theoretical capacity are regarded as promising anodes for sodium-ion batteries (SIBs) but encounter several challenges because of the complex conversion process, which leads to numerous side reactions and the inevitable disintegration of active materials, thereby impeding practical application. In this work, inspired by a three-dimensional (3D) structure design, a stable 3D reduced graphene oxide with heteroatom-sites coordinated carbon centers (3DNSrGO) is fabricated, which features uniform and abundant nickel sulfide (NiS) particles within the empty spaces, along with sufficient access to the liquid electrolyte, thereby enabling more efficient transfer of sodium ions. Moreover, the combination of the polypropylene (PP) membrane and glass fiber (GF) separator effectively reduces sodium polysulfide shuttling, prevents sodium metal corrosion, and resolves short-circuiting issues. Benefiting from the three-dimensional porous structure and simultaneous optimization at the battery level, the nickel sulfide anode demonstrates improved rate capability (specific capacity of 386 mAh/g at 10 A/g) and long-term cyclic stability over 2000 cycles. This study holds considerable potential for addressing (1) the growing requirement for efficient and sustainable Na+ host materials, and (2) a newfangled approach that optimizes the long-term cyclic stability of SIBs via a better cell configuration.