Defect (mainly vacancy) engineering has shown its potential for modulating the functional behavior of magnetic materials. In this work, dense Ni vacancies are introduced in Ni45Mn36.5In13.5Co5 alloy and the effect of these vacancies on the magnetic properties is both theoretically and experimentally clarified. In detail, Ni vacancy with the lowest formation energy is introduced by high energy electron irradiation, which shortens the distance between adjacent Mn atoms to strengthen the interaction between them and increase the corresponding magnetic moments, leading to the dTm/dH increase from −2.89 to 6.28 KT−1. As a result, a breakthrough in the magnetocaloric performance is correspondingly achieved, i.e., the entropy change (ΔSM) increases up to an ultra-high value of 48.15 J/(kg·K), much higher than all other reported values. Moreover, the reversible magnetostrain is also improved from 80 to 200 ppm. In summary, this work provides strong guidance for optimizing the magnetic performance of Ni–Mn based Heusler alloys via vacancy modulation.