A novel in-situ non-flatness measurement method of wafer chuck in step-and-scan projection lithographic tool is presented. The local heights of wafer surface are measured by the linear variable differential transformer (LVDTs) when the different offsets between wafer and wafer chuck exist. A temporary boundary condition is built to calculate the relative non-flatness of wafer chuck line by line and eliminate the effect of the wafter surface shape with recursion formula. The height difference of the neighboring columns is calculated with recursion formula, which is added to each row to remove the temporary boundary condition limitation and the coarse non-flatness of wafer chuck with the same height is determined. According to the coarse result, the four neighboring points of the measured point are used as reference to approach the accurate non-flatness of wafer chuck with the least square method. Computer simulation and experimental results prove that the calculated result accords with the real non-flatness of wafer chuck well, and the reproducibility by this method is better than 0.3 nm. The method is also valid for measurement of wafer surface shape.