Spatially-resolved electron energy-loss spectroscopy (EELS) is applied to the multilayer (SiO2/Si3N4/SiOxNy/Si), a common semiconductor device structure. To observe depth profile at sub-nanometre spatial resolution, scanning transmission electron microscopy (STEM) and energy-filtering transmission electron microscopy (EFTEM)-based techniques are compared in practical application. STEM-based EELS is useful in simultaneously analysing plural elements. EFTEM-based EELS is suitable for analysing the chemical shift and core loss intensity of single element. The practical spatial resolution is of the same order for each technique, both involving beam damage, which can be reduced by decreasing current density in EFTEM and avoiding beam overlapping in STEM.