Ge-based anodes have been considered as an alternative to graphite for lithium-ion batteries because of their high theoretical capacities. Nonetheless, their performance is still not up to the requirements of practical application. Herein, a novel Ge12Ni19 @nitrogen-doped carbon microflowers (Ge12Ni19 @NCFs) composite with subtle hierarchical structure was successfully fabricated based on carbon framework confinement and transition-metal alloy strategies. Detailed analysis was conducted on its unique structure and composition through various characterizations. Meanwhile, control tests proved that the nitrogen-doped carbon framework can improve the cycle stability effectively. Furthermore, density functional theory (DFT) calculations reveal that alloying with Ni is conducive to accelerating electron migration and Li+ diffusion of Ge anode. Benefiting from the synergistic effects, the Ge12Ni19 @NCFs composite exhibited a remarkable lithium storage performance. After cycled 1000 times at 2 A g−1, it still delivered a high capacity of 541 mAh g−1 with a retention of 90%.