Electronic structures of pyrites containing vacancies were calculated using a first-principles plane-wave pseudopotentials method. The influence of vacancy defects on pyrite flotation behavior is discussed. Results show that sulfur vacancy has little effect on volume while iron vacancy results in a cell volume expansion of 1.29%. The presence of vacancy defects mainly affects the electronic structure near the Fermi level while new energy levels are introduced into the forbidden band and this is caused by atoms close to vacancies. The presence of vacancies increases the Fermi level, which is undesirable in pyrite flotation. The calculation of effective mass indicates that the presence of vacancies increases the localization of electrons located at the bottom of the conduction band. Mulliken bond population analysis of atoms shows that the covalence of the S—Fe bond is greater than that of the S—S bond and that the presence of vacancies results in an increase in the covalence of bonds between the atoms close to the vacancies, which is beneficial to pyrite flotation. We conclude that the presence of vacancies adversely affects pyrite flotation when both the influence of vacancies on the Fermi level and the covalence between atoms are considered.