There are crucial demands for high power density and long-term cycling performance of Li-ion batteries (LIBs), and the development of stable electrode material operating at high current densities still remains a challenge. Here we develop a novel strategy for the synthesis of flexible N-doped carbon nanofiber/CoFe2O4 film (CoFe2O4@N-CNF) with a double-layer carbon protection by electrospinning, which possesses stable carbon shell and honeycomb-like core with CoFe2O4 nanosheets embedded into conductive and interconnected carbon nanosheets. The unique structure is beneficial for providing robust structural stability upon long-term cycling, and offering nitrogen-rich interconnected mesoporous and conductive carbon matrix for fast charge and ion transport. As a consequence, the optimized CoFe2O4@N-CNF exhibits a high reversible capacity of 858 mAh g−1 at 0.1 A g−1, excellent rate capability (306 mAh g−1 at 30 A g−1), and superior cycling stability up to 10,000 cycles with almost no capacity loss at 10 A g−1. We believe that this proposed methodology has a profound impact on drastic improvements of various flexible energy storage devices.