Hybrid multi-shelled nanostructures with tailored shell architectures have shown great promise for electrochemical energy storage applications. However, formation of such designed delicate architectures remains a great challenge. Here, starting from metal-organic frameworks (MOFs), we report a facile and straightforward, in situ chemical transformation strategy, to fabricate a Ni@NCNTs hybrid multi-shelled structure with complex shell architecture. Then, a promising anode material consisting of NiS nanocrystals embedded in multi-shelled hollow microspheres (MSHMs) interlinked by N-doped carbon nanotubes (NCNTs) was prepared through the manipulation of template engaged reaction by using the urea and yolk-shelled Ni-MOFs precursor. The rationally designed NiS@NCNT MSHMs not only provide sufficient electrode/electrolyte contact area, short mass/charge transfer distances and improve the electron transportation efficiency, but also release the volume expansion effectively owing to the multi-cavities within the hollow structure. Benefiting from the unique structural merits, the NiS@NCNT MSHMs yields a high reversible specific capacity of 531.5 mAh g−1 at 0.05 A g−1, stable cycling with 89.3% capacity retention over 500 cycles at 1 A g−1, and excellent rate capability. In addition, in situ XRD reveals that the initial sodium storage processes in NiS is based on an intercalation reaction, then a two-step conversion reaction. Our work reveals the importance of rational design and synthesis of multi-shelled hollow nanostructures with higher complexity for improved electrochemical performance.