In response to the severe blocks of the large volume change and sluggish capacity decay originating from the Lithium ion insertion/extraction in the anodes of Lithium ion batteries, transition metal oxides with high cycle stability are desirable yet extremely challenging for achieving high energy density anodes. Here, we report that a double-shelled NiO nanocrystal-doped MnO layer with robust defects, epitaxially grown on a nanoporous Ni network by simultaneously dealloying and oxidising NiMn alloy, can overcome these challenges to deliver a large capacity with excellent cycle stability. The interconnected core-shell nanoporous structure with robust defects possesses ultrahigh efficient electron/ion transport and a volume buffer. Consequently, the free-standing electrode as a whole delivers a highly reversible capacity of 1172 mAh cm−3 (960 mAh g−1) with a remarkable cycle life (105% retention after 200 cycles at 100 mA g−1). Furthermore, the electrode achieves a high capacity of 831.5 mAh cm−3 (681 mAh g−1) even at 1000 mA g−1, demonstrating a high rate capability. The proposed synthetic strategy can be further explored for the construction of other three-dimensional metal@metal oxide electrodes for application in next-generation energy storage systems.