With the development of semiconductor manufacturing to 1x nm technological node, focus control accuracy of lithography needs to meet dozens of nanometers. In the range of nanoscale, integrated circuit (IC) process on silicon wafer has an important impact on the measurement accuracy of the focusing and leveling system. A process dependent error model is established based on actual focusing and leveling optical system model, trigonometry and Moire measurement principle. Research shows that process dependent error mainly results from the multiple reflections inside the photoresist. Simulation is conducted with three different photoresists. The simulation results indicate that process dependent error of different photoresists has the same trend as the photoresist thickness and process dependent error decreases with the increase of incident angle (45°~85°). Seven processed silicon wafers are measured on the experimental setup. The statistical mean of the difference between the experimental measurement and the theoretical model calculation is less than 6 nm. The results show that, in order to reduce the process dependent error, it is necessary to increase the angle of incidence of focusing and leveling system in lithography and improve the uniformity of the photoresist coating.