Lattice strains near the Si/NiSi2 interface and their effects on electron energy-levels of Si were investigated via experimental and theoretical approaches. For highly spatially resolved analysis, electron nanoprobe techniques were employed: convergent beam electron diffraction (CBED) for lattice strain and electron energy-loss spectroscopy (EELS) for the electron energy-levels. Additionally, a theoretical analysis based on the density-functional theory (DFT) was performed to explain the experimental results. The actual distribution of the lattice strains was complicated; both tensile and compressive strains were found to coexist near the interface. Shifts in the Si L 23-edge of the EEL spectra were found to be induced by the lattice strain. Finally, we described the “distribution of the electron energy-levels” as the strain distribution around the interface in a submicron region.