Thin-walled workpiece is prone to produce deformation in the process of machining because of cutting and clamping forces. In this paper, a model of cutting parameters optimization is proposed to control the deflection. The influence of deflection on nominal milling depth is taken into account and the machining deflection is computed by iterative method. Based on the optimization model, a prototype system is developed to optimize the cutting parameters for a thin-walled workpiece with the genetic algorithm and finite element method. Finally, a simulation example is used to demonstrate the feasibility of the cutting parameters optimization method. The simulation result can be further employed into practical machining situation.