Hybrid substrates comprising both silicon-on-insulator (SOI) and bulk Si regions have been fabricated using the technique of patterned separation by implantation of oxygen (SIMOX) with high-dose (1.5 × 1018 cm−2) and low-dose ((1.5–3.5) × 1017 cm−2) oxygen ions, respectively. Cross-sectional transmission electron microscopy (XTEM) was employed to examine the microstructures of the resulting materials. Experimental results indicate that the SOI/Si hybrid substrate fabricated using high-dose SIMOX is of inferior quality with very large surface height step and heavily damaged transitions between the SOI and bulk regions. However, the quality of the SOI/Si hybrid substrate is enhanced dramatically by reducing the implant dose. The defect density in transitions is reduced considerably. Moreover, the expected surface height difference does not exist and the surface is exceptionally flat. The possible mechanisms responsible for the improvements in quality are discussed.