We report nitric oxide ion (NO+) beam induced nanoscale pattern formation on Si (100) surface. The patterns are found to be structurally as well as chemically periodic. A highly reactive 14 keV NO+ beam is developed in an Electron Cyclotron Resonance ion beam system and implanted on Si (100) surface at oblique angles to form a periodic nano-ripple pattern with specific silicon oxide and silicon oxy-nitride enriched sectors with different dielectric constants. Well-defined ripple patterns start to form at comparatively lower ion fluences due to an additional instability generation by the chemical reaction of NO+ ions with silicon. The chemical shift of the Si 2p peak in the x-ray photoelectron spectroscopy study of an ion irradiated sample confirms the formation of silicon oxide and silicon oxy-nitride, whereas the local chemical nature of the ion induced ripple patterns, probed by electron energy loss spectroscopy, approves spatially resolved silicon oxide and silicon oxy-nitride stripe pattern formation. The ion modified layer thickness measured by cross-sectional transmission electron microscopy has an excellent agreement with Monte Carlo simulations. The optical sensitivity of an NO+ bombarded chemically patterned Si surface is also studied by UV–Visible spectroscopy. Formation mechanisms and potential applications of such nano-scale spatially graded materials are discussed.