Designing a unique morphology and nanoarchitecture with a heterostructure is regarded as an efficient strategy to achieve lithium-ion batteries (LIBs) with high capacity and cycle life. Herein, N-doped C-encapsulated flower-like NiS/Ni3(BO3)2 heterostructures (NiS/Ni3(BO3)2/NC) with a core-shell morphology are successfully synthesized by a facile general method to improve the rate performance and prolong the cycle life of LIBs. The coated NC layer and core-shell structure with elasticity can relieve the volume expansion during the lithiation/delithiation process to strengthen the stability of the structure. Moreover, the NC layer and NiS/Ni3(BO3)2/NC heterostructure can enhance the electronic conductivity of the electrode and guarantee fast and unimpeded electron transfer channels, thereby improving the electrochemical reaction kinetics. Owing to the synergy of heterostructures and core-shell layer, the as-synthesized NiS/Ni3(BO3)2/NC anode acquires a specific charge capacity of 549 mA h g-1 at 0.2 A g-1 after 100 cycles; meanwhile, a reversible capacity of 322 mA h g-1 can be maintained even at 1 A g-1 after 500 cycles. This study develops a universal interface manipulation strategy for the synthesis of M3B2O6-based or/and other advanced transition metal compound anode materials for the practical applications of LIBs.