The electronic structures of clusters Co6(μ3-E)8(CO)6(E:-S,-Se) have been calculated by using the DV-SCC-Xα method. The calculated results show that there are two types of MO energy distribution. Below -13eV forⅠ, the distribution of MO energies are discrete and sparse, but above the value (-13eV), the energy levels of their MO are relatively very dense levels. The same is true of clusterⅡ (-14eV). Also the MO energies belonged to Co-Co bonding all lie in the highest energy group but those belonged to Co-E bonding are more sparse and low. Finally, the negative or positive charge of atoms in cluters also is significant. Co charged 0.39(Ⅰ) and 0.26(Ⅱ), face-bridging S 0.54, Se 0.73, terminal carbonyl C-1.01(Ⅰ) and -1.14(Ⅱ). These festures are related to their chemical properties under discussion.