Manganese fluoride (MnF2) is a high‐performance lithium‐ion battery anode material with an excellent structural stability, low synthesis cost, and better manufacturing convenience. However, its low theoretical capacity (577 mAh g−1), weak conductivity of fluoride, and poor recyclability limit its practical application. Fortunately, oxygen vacancies (Ov) and heteroatomic doping are among the most promising strategies to modulate the inherent reduced electronic conductivity and kinetic response of electrode materials in order to boost their lithium storage capacity. Herein, self‐templating, self‐optimizing, and self‐supporting metal–organic framework template approach with the introduction of oxygen vacancies by substitution of exogenous heteroatoms is proposed, where triple heteroatom‐doped (N, O, and F) carbon‐encapsulated MOF‐derived manganese fluoride (Ov‐ZMF@NOFs) microstructures are designed. Interestingly, the exogenously introduced triple heteroatomic carbon matrix forms a fluffy three‐dimensional mechanical structure, interlaced conducting networks, efficient conducting pathways, and intense electrochemical dynamics at the periphery of the manganese fluoride nanoparticles. Benefiting from the above‐mentioned features, the Ov‐ZMF@NOFs exhibit expected electrochemical properties with ultra‐long recyclability (high reversible capacity of 419 mAh g−1 at 6 A g−1) and good rate performance (capacity of 232 mAh g−1 at a current density of 16 A g−1). Theoretical calculations underline the essential contribution of multiple heteroatoms doping in boosting the electrode conductivity and reducing the lithium‐ion migration energy barrier. Combining controllable vacancy engineering and heteroatom doping technology at the nanoscale provides a new philosophy and concept for the design and fabrication of next‐generation high‐energy lithium‐ion battery materials.