n-type 6H-SiC (0001) single crystal substrates were implanted with three fluences of manganese (Mn+) ions: 5×1015, 1×1016 and 5×1016cm−2 with implantation energy of 80keV at 365°C to stimulate dynamic annealing. The samples were characterized using Rutherford backscattering channeling spectroscopy (RBS/C), high-resolution X-ray diffraction technique (HRXRD), and Superconducting Quantum Interference Device (SQUID) techniques. Two main defect regions have been identified using RBS/C spectra fitted with the McChasy code combined to SRIM simulations. Intermediate defects depth region is associated with vacancies (DV) and deeper defect (DN) essentially related to the Si and C interstitial defects. The defect concentration and the maximum perpendicular strain exhibit similar increasing trend with the Mn+ fluence. Furthermore, the amount of Mn atoms at Si substitutional sites and the corresponding magnetic moment per Mn atom were found to increase with increasing Mn fluence from 0.7μB to 1.7μB and then collapsing to 0.2μB. Moreover, a strong correlation has been found between the magnetic moment and the combination of both large DV/DN ratio and high Mn at Si sites. These results are corroborated by our ab initio calculations considering the most stable configurations showing that besides the amount of Mn substituting Si sites, local vacancy-rich environment is playing a crucial role in enhancing the magnetism.