The purpose is to study the influence of the height difference of the substrate surface on the flatness of the workpiece and determine the double-sides processing effectiveness of ultra-thin sapphire wafers. Obtain the different height differences of baseplates with different surfaces (height difference of 5.3 μm, 9.8 μm, 19.9 μm, 29.7 μm) through various methods. By using the layer stacked clamping to clamp the ultra-thin sapphire wafer (thickness 0.17 mm) and perform double-sides processing, thus obtaining the flatness of the workpiece under different height differences. The two-layer processing of ultra-thin sapphire wafers is carried out by using the layer stacked clamping method and paraffin bonding method respectively, and the effectiveness of the layer stacked clamping method is verified through comparative experiments. The result shows that the flatness of ultra-thin sapphire wafers increases with the increase of height difference under four different surface height differences, but the increasing trend is far less than the base plate flatness change trend. Layer stacked clamping method and the paraffin bonding method can realize the double-plane processing of ultra-thin sapphire, and the difference between them is small. The layer stacked clamping method can finally obtain a smooth surface with surface roughness Ra=1.4 nm and flatness PV=0.968 μm. Through experimental analysis and verification, it is proved that the height difference of the baseplate surface should smaller than the target flatness of the ultra-thin sapphire wafer. The layer stacked clamping method is equivalent to the paraffin bonding method in processing effect, but the processing efficiency per unit time is higher than the paraffin bonding method, which has a good engineering application prospect.