The spin-resolved electronic states and spin polarization of a benzene molecule adsorbed on an Fe(100) surface are investigated using spin-polarized metastable-atom deexcitation spectroscopy (SPMDS) measurements and density functional calculations. The spin asymmetry observed by the SPMDS is found to be negative at the induced pi* states close to the Fermi level and positive in molecular orbitals. The opposite spin asymmetry can be explained well by the calculated spin density distributions and plane-averaged density of states on the vacuum side. It is also found that the energy region of the negative spin asymmetry increases with increasing coverage of the benzene molecule. This phenomenon has been discussed in conjunction with the possible multiple adsorption sites, followed by an argument for the site-dependent spin polarization.