The fabrication of X-ray grating and silicon-based micro-channel plate on the large area silicon wafer involves the thermal oxidation of silicon which can greatly deform the wafer with microstructures of high-aspect-ratio, hindering the practical applications of the silicon-based devices. The thermal oxidation deformation of a 5-inch silicon wafer was experimentally studied and the mechanical factors affecting the deformation were analyzed. The method to decrease the deformation was also provided. The wafers with microstructures of high aspect-ratio were firstly fabricated by use of the photo-assisted electrochemical etching technique, and then different thermal oxidation methods were experimented, and lastly the deformation was compared. The results show that the deformation of large area silicon wafer can be decreased greatly by adjusting the thermal oxidation temperature to minimize the thermal expansion coefficient and by exerting an external force on silicon wafer during the thermal oxidation process.