Manganese selenide (MnSe), as a newly emerged manganese‐based chalcogenide, has recently been considered as a potential cathode for aqueous Zn‐based energy storage due to its many merits. Nevertheless, its unsatisfactory kinetic performance and cycling stability, along with its controversial energy storage mechanism, hinder its commercial application. Herein, the MnSe microspheres with Se‐rich vacancies (VSe‐MnSe) are synthesized, and employed as a cathode for Zn‐ion batteries/capacitors (ZIBs/ZICs) for the first time. Density functional theory (DFT) calculations and kinetic analyses illustrate that vacancy engineering of MnSe enhances the active sites, improves the electronic conductivity and ion transport, and reduces the adsorption energy and diffusion energy barriers of H+ and Zn2+, endowing the VSe‐MnSe cathode of ZIBs with significantly enhanced specific capacity, rate capability, and cycling stability. Interestingly, ex situ tests confirm the stable existence of VSe‐MnSe during the whole charge/discharge process and store energy with the first H+ insertion and subsequent H+/Zn2+ co‐insertion. More encouragingly, the VSe‐MnSe//porous carbon (PC) ZICs exhibit an ultrahigh energy density (178.0 Wh kg−1), a high power density (10 kW kg−1), and eminent cyclic stability (up to 10000 cycles). This research offers an efficient strategy for designing and developing high‐performance manganese‐based chalcogenides and sheds new insights into their energy storage mechanisms.