As the critical dimensions in the semiconductor industry were shrinking,the influences of wafer flatness on lithographic performance became increasingly greater. Based on the imaging performance of the special marks,the relationships between alignment offsets and wafer height offsets were discussed. Then,a novel method for measuring the wafer flatness was presented. Experiments show that wafer flatness and the surface topography can be measured in situ by the technique with high accuracy. Taking into account of the nonuniformity of the adsorption power of vacuum chuck,wafer flatness can be measured with high accuracy. Compared to the level sensor based method,the spatial resolution is increased by 67%. The surface topography of the wafer can be obtained by the new method.