The mechanism of Schottky-barrier height (SBH) tuning by yttrium (Y) segregated at nickel silicide (NiSi2)/silicon interface is investigated based on first-principle calculations. SBH modification can be explained by a new chemical structure that forms when Y atoms substitute silicon atoms near the interface. Silicon dangling bonds are saturated, leading to a new pinning-free interfacial structure. When other layers of Y atoms are segregated in , SBH for electrons can be reduced from 0.65 to 0.1 eV. The previously reported experimental phenomena can be explained by the calculations.