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As key components of lithium-ion batteries (LIBs), anode materials can determine the capacity, stability, and safety of LIBs. Transition metal oxides have been regarded as promising LIB anodes due to their low cost, natural abundance, and substantial theoretical capacity. Nevertheless, the large-scale use of metal oxides is hampered by their intrinsic demerits, including low conductivity and large volume fluctuation. Several strategies have been proposed to address these limitations, such as morphological/structural design, heterostructuring, and defect engineering. It’s feasible to integrate the above strategies by using suitable self-sacrificial templates. Owing to their multiformity, porosity, and large surface area, metal-organic frameworks (MOFs) remain suitable templates for metal oxide fabrication. Herein, this work develops a series of oxygen-deficient (FeCoNi)3O4 using different MOFs (terephthalic acid, 1,3,5-benzenetricarboxylic acid, and pyromellitic acid) as self-sacrificial templates (denoted as FCNO-PTA, FCNO-BTC, and FCNO-PTC, respectively). Both experimental and theoretical studies reveal that abundant oxygen vacancies can create local built-in electric fields. This not only provides additional lithium adsorption sites but also facilitates the formation of a robust solid electrolyte interface (SEI), thereby mitigating the lattice strain upon lithiation/delithiation and enhancing overall performance. Remarkably, FCNO-PTC demonstrates the optimal reversible capacities (1176 mAh g–1 at 0.2 A g–1 after 150 cycles; 725 mAh g–1 at 1 A g–1 after 350 cycles) due to its higher oxygen vacancy content. This work provides new insights into the optimisation of metal oxides at an atomic scale.