We performed detailed analysis of nickel silicide discontinuities induced by agglomeration, which causes the increased electric resistance in high-performance complementary metal–oxide–semiconductor devices, by using advanced physical analysis techniques: transmission electron microscopy (TEM), scanning electron microscopy (SEM) electron backscatter diffraction (EBSD) analysis, and three-dimensional atom-probe (AP) analysis. We confirmed that the agglomeration of the nickel silicide is related to elongated-triangular-shaped splits, which cause discontinuities that occur at low-angle grain boundaries pinned by boron clusters even with small stress. We successfully determined the formation mechanism of these nickel silicide discontinuities in detail.