The site preference of 3d transition metals in B2-NiAl intermetalics and its effects on bond characters are investigated by the pseudopotential plane wave method. The formation energy results show that Sc, Ti, V and Zn prefer to occupy the Al site, while Cr, Mn, Fe, Co and Cu prefer to occupy the Ni site in NiAl. By analyzing changes in crystal lattice constants, Mulliken population, overlap population and valence charge density, the crystal lattice distortion and bond characters are discussed. The results show that the lattice distortions of Sc, Ti, V and Zn doped NiAl play an important role in determining the alloy properties. The strong repulsion interaction and anti-bonds as well as charge transfer between the dopant atom and the nearest_neighbor Ni atoms are observed, which makes the fraction of covalent bonds to be decreased and the fraction of the metallic bonds to be increased by Sc, Ti, V and Zn substituting the Al sites of NiAl. The bond character changes a little by Cr, Mn, Fe, Co and Cu substituting the Ni sites of NiAl.