The surface phonons of LaB6(100) surface have been investigated by means of high resolution electron energy spectroscopy. On the clean surface we have observed 8 loss peaks in the off-specular spectra, of which the higher energy losses are related to the vibrations of the three-dimensional network of boron. Theoretical analysis based on a force constant model strongly suggests the deformation of the three-dimensional network of boron; the topmost octahedra are expanded by approximately 0.004 nm parallel to the surface.