For dams and rock foundations of ages, the actual mechanical parameters sometimes differed from the design and the experimental values. Therefore, it is necessary to carry out the inversion analysis on main physical and mechanical parameters of dams and rock foundations. However, only the integrated deformation modulus can be inversed by utilizing the conventional inversion method, and it does not meet the actual situation. Therefore, a new method is developed in this paper to inverse the actual initial zoning deformation modulus and to determine the inversion objective function for the actual zoning deformation modulus, based on the dam displacement measured data and finite element calculation results. Furthermore, based on the chaos genetic optimization algorithm, the inversion method for zoning deformation modulus of dam, dam foundation and, reservoir basin is proposed. Combined with the project case, the feasibility and validity of the proposed method are verified.