The effect of structural and chemical disorder on magnetism of Mn-implanted 3C-SiC epilayer on Si(100) is investigated experimentally using Rutherford backscattering channeling spectroscopy (RBS/C), x-ray diffraction (XRD), micro-Raman spectroscopy $(\ensuremath{\mu}\text{RS})$, and magnetometry, and theoretically using ab initio calculations. A single 3C-SiC epilayer on Si(001) was implanted at room temperature (RT) with Mn ions at 80 keV and at a dose of $5\ifmmode\times\else\texttimes\fi{}{10}^{15}\text{ }{\text{cm}}^{\ensuremath{-}2}$. RBS data show the formation of a highly disordered implanted layer of $\ensuremath{\sim}45\text{ }\text{nm}$ with a peak Mn atomic concentration of $\ensuremath{\sim}1.8%$ randomly distributed, in agreement with the stopping and range of ions in matter (SRIM) simulation. The experimental results of magnetic moment per Mn are interpreted by assuming that the implanted layer consists of two respective main regions, C--rich and Si--rich regions, as reflected by the presence of a graphitic phase, in which the local atomic environment of Mn is essentially C. Annealing seems to favor Mn substitution into Si sites, indicated by the substantial expansion of the lattice constant due to larger covalent Mn radius as observed by XRD and due to a high local tensile strain determined from $\ensuremath{\mu}\text{RS}$. This interpretation is also supported by recent calculations, showing that it is energetically favorable for Mn to substitute Si sites. The temperature dependence of magnetization shows an insulatinglike character for the as-implanted film and metalliclike for the annealed-implanted film with Curie temperature above RT. In addition, the magnetic moment per Mn increases strongly with annealing from 0.23 to $0.65{\ensuremath{\mu}}_{\text{B}}$. The experimental behavior is supported by our ab initio calculations, showing that magnetism in Mn-doped 3C-SiC can be enhanced by carefully growing a structure with Mn in Si sites using a C-deficient SiC host, possibly resulting in localized magnetic interactions.