Si wafers with a 220 nm top oxide layer were sequentially implanted at room temperature with 40 keV He and 35 keV H ions at fluence of 5× 10^16/cm2 and 1× 10^16/cm2, respectively. Techniques of scanning electron microscopy, atomic force microscopy and cross-sectional transmission electron microscopy (XTEM) were used to characterize the thermal evolution of surface damage as well as defect microstructures. Surface blisters as well as the localized exfoliation (~ 0.42 μm in depth) have been observed for samples annealed at temperatures of 500 ℃ and above. XTEM observations reveal a variety of defect microstructures, including cavities, platelets, nanometer or micrometer sized cracks and dislocations. The platelets and cracks are mainly distributed at the depth of about 0.42 μm parallel to the sample surface, which are responsible for the occurrence of the observed surface features. The relations between surface damage and defect microstructures are described in detail.