We report mixed (CO+ and N2 +) ion beam induced spatially varying chemical phases formation on Si (100) surface in nanometer length scale. Simultaneous bombardment of carbon, oxygen and nitrogen like three reactive ions leads to well-defined ripple development and spatially varying periodic chemical phases formation. Post bombardment chemical changes of Si surface are investigated by x-ray photoelectron spectroscopy, and spatially resolved periodic variation of chemical phases are confirmed by electron energy loss spectroscopy. The thickness of ion modified amorphous layer, estimated by Monte Carlo simulation (SRIM), is in excellent agreement with the cross-sectional transmission electron microscopy measurements. The formation of such periodic nanoscale ripple having multiple chemical phases at different parts is explained in terms of chemical instability, local ion flux variation and difference in sputtering yield. Potential applications of such newly developed nano material are also addressed.