We have investigated the effect of argon (Ar) plasma treatment on the surface of graphite and the hydrothermal growth of zinc oxide (ZnO) microstructures. With the plasma treatment, the growth behavior of ZnO microrods on the graphite substrates changed drastically. After the graphite surface was exposed to the Ar plasma, the number density of ZnO was one order of magnitude higher than that on the pristine graphite without plasma treatment. Raman spectroscopy revealed that Ar plasma treatment created the structural defects on the graphite surfaces and decreased the mean distance of defects. Surface characterization through atomic force microscopy and X-ray photoelectron spectroscopy showed that the graphite surface was roughened and that oxygen-carbon bonding was formed. The enhanced nucleation of ZnO can be explained by the generation of structural defects, surface roughness, and surface functional groups on the graphite substrate. Therefore, Ar plasma treatment can be used as a simple method to engineer the surface properties of graphite substrates and to control the crystal nucleation and growth of inorganic materials on their surface.