Manganese-based oxide electrode materials suffer from severe Jahn-Teller (J-T) distortion, leading to severe cycle instability in sodium ion storage. However, it is difficult to adjust the electron at d orbitals exactly to a low spin state to eliminate orbital degeneracy and suppress J-T distortion fundamentally. This article constructed concentration-controllable Mn/O coupled vacancy and amorphous network in Mn3O4 and coated it with nitrogen-doped carbon aerogel (Mn3−xO4−y@NCA). The existence of Mn/O vacancies has been confirmed by scanning transmission electron microscopy (STEM) and positron annihilation lifetime spectroscopy (PALS). Atomic absorption spectroscopy (AAS) and X-ray photoelectron spectroscopy (XPS) determine the most optimal ratio of Mn/O vacancies for sodium ion storage is 1:2. Density functional theory (DFT) calculations prove that Mn/O coupled vacancies with the ratio of 1:2 could exactly induce a low spin states and a d4 electron configuration of Mn, suppressing the J-T distortion successfully. The abundant amorphous regions can shorten the transport distance of sodium ions, increase the electrochemically active sites and improve the pseudocapacitance response. From the synergetic effect of Mn/O coupled vacancies and amorphous regions, Mn3−xO4−y@NCA exhibits an energy density of 37.5 W h kg−1 and an ultra-high power density of 563 W kg−1 in an asymmetric supercapacitor. In sodium-ion batteries, it demonstrates high reversible capacity and exceptional cycling stability. This research presents a new method to improve the Na+ storage performance in manganese-based oxide, which is expected to be generalized to other structural distortion.