Density functional theory calculations have been carried out to investigate the electronic structures and the alpha/beta relative stability of Keggin-typed [XW12O40](n-) anions with transition metal as heteroatom X (X = Cr-VI, V-V, Ti-IV, Fe-III, Co-III, Ni-III, Co-II and Zn-II). Nice agreement in geometries between computation and experiment has been obtained, and the higher stability of the alpha isomer over the beta one has been confirmed. Structural parameter analysis reveals that the {M3O13} triads in both alpha and beta isomers contract considerably with the increase of the negative anionic charge, while the overall size of both isomers shrinks only slightly. Fragment molecular orbital analysis shows that except alpha/beta-[TiW12O40](4-), the electronic structures of Keggin anions can be described by the insertion of the e and/or t(2) orbital of XO4n- into the frontier orbitals of W12O36 cage, and this leads to the specific redox property, which is different from that of the Keggin anions with main-group elements as heteroatoms. Energy decomposition analysis shows that the enhanced intrinsic stability of the alpha isomer in T-d arrangement of W12O36 shell and the larger deformation of the alpha over the beta isomer are two dominating factors and contribute oppositely to the alpha/beta relative stability.