Three-dimensional holey nitrogen-doped carbon matrixes decorated with molybdenum dioxide (MoO2) nanoparticles have been successfully synthesized via a NaCl-assisted template strategy. The obtained MoO2/C composites offered multi-advantages, including higher specific surface area, more active sites, more ions/electrons transmission channels, and shorter transmission path due to the synergistic effect of the uniformly distributed MoO2 nanoparticles and porous carbon structure. Especially, the oxygen vacancies were introduced into the prepared composites and enhanced the Li+ intercalation/deintercalation process during electrochemical cycling by the Coulomb force. The existence of the local built-in electric field was proved by experimental data, differential charge density distribution, and density of states calculation. The uniquely designed structure and introduced oxygen vacancy defects endowed the MoO2/C composites with excellent electrochemical properties. In view of the synergistic effect of the uniquely designed morphology and introduced oxygen vacancy defects, the MoO2/C composites exhibited superior electrochemical performance of a high capacity of 918.2 mAh g–1 at 0.1 A g–1 after 130 cycles, 562.1 mAh g–1 at 1.0 A g–1 after 1000 cycles, and a capacity of 181.25 mAh g–1 even at 20.0 A g–1. This strategy highlights the path to promote the commercial application of MoO2-based and other transition metal oxide electrodes for energy storage devices.