Wide bandgap semiconductors doped with transition metals are attracting significant attention in the fabrication of dilute magnetic semiconductor devices (DMSs). The working principle of DMSs is based on the manipulation of the electron spin, which is useful for magnetic memory devices and spintronic applications. Using the density functional theory (DFT) calculation with the GGA+U approximation, we investigated the effect of native defects on the magnetic and electronic structure of Mn+2-doped 3C-SiC structure. Three structures were selected with variations in the distance between two impurities of (Mn+2)-doped 3C-SiC, which are 4.364 Å, 5.345Å, and 6.171 Å, respectively. We found ferromagnetic coupling for single and double Mn+2 dopant atoms in the 3C-SiC structure with magnetic moments of 3 μB and 6 μB respectively. This is due to the double exchange because of p-d orbital hybridization. The p-orbitals of C atoms play important roles in the stability of the ferromagnetic configuration. The impact of Si-vacancy (nearby, far) and C-vacancy (near) of (Mn+2)-doped 3C-SiC plays an important role in the stabilization of AFM due to super-exchange coupling, while the C-vacancy (far) model is stable in FM. All electronic structures of Mn+2-doped 3C-SiC reveal a half-metallic behavior, except for the Si-vacancy and C-vacancy of (nearby), which shows a semiconductor with bandgap of 0.317 and 0.828 eV, respectively. The Curie temperature of (Mn+2)-doped 3C-SiC are all above room temperature. The study shows that native vacancies play a role in tuning the structure from (FM) to (AFM), and this finding is consistent with experiments reported in the literature.