In this paper nanometer-sized particles of Si3N4 deposited on the surface of a highly oriented pyrolytic graphite (HOPG) under ultrahigh vacuum conditions have been observed. The reproducible scanning tunneling microscope (STM) topographic images show a two-dimensional ordered structure with a hexagonal close-pack lattice that covered a much smaller area of the HOPG surface. The lattice constant is about 24 nm, which is comparable to the sizes of the nanoparticles observed by transmission electron microscopy and is about 100 times that of the HOPG’s constant. A physical interaction is suggested to exist between the nanoparticles and substrate. The STM results demonstrate the anomalous electrical conductive mechanism during the experiment of the ceramic nanoparticles; however, Si3N4 in bulk form is an insulating material. The origin for the distortion of the images is discussed as well.