To investigate the origin of vacancies in SiC nanopowders, complex theoretical and experimental investigations of SiC nanopowders of different geometry sizes were carried out. Our theoretical approach included ab initio band energy calculations and molecular dynamics simulations with dynamic boundary conditions. Experimental methods included EPR spectra. The significant influence of nanocrystallite and grain sizes on the concentration and type of vacancies is demonstrated. On the other hand, our comparison of experimental data and theoretical simulations show that vacancies influence the optical properties of SiC nanocrystallites.