To ensure the reliability of the wafer stage system of lithography, all factors affecting the wafer stage system reliability were analyzed. A new method based on experts grading method[1] and analytic hierarchy process(AHP)[2] is developed to allocate the reliability indices of wafer stage system. This approach considers not only the experience and knowledge of the expert, but also combines the Comparative Matrix of analytic hierarchy process to reduce the defect that stronger subjective factors of experts grading method. Finally, the wafer stage system of a certain lithography was taken as an example, and the reliability allocation of the system was obtained. The result indicate that the proposed method is feasible and effective.