We have observed simple oscillations in three-dimensional (3D) patterns of electron thermal diffuse scattering (separated from electron-electron energy loss) measured on a Si(001) surface. We interpret these oscillations as coherent interference within a small cluster of atoms in which vibrational correlation within the nearest neighbors (NN) is dominant. A 3D Patterson function analysis of the oscillation reveals the atomic structure of the Si(001) surface consisting of NN pairs including dimers. This finding provides a promising new clue to determine the structures of bulk and the surface of solids.