A new method to perform the apportionment of system reliability with Genetic Algorithm（GA）and Fuzzy Logic（FL）is presented. We employed FL to model the uncertainty Within the limits and designing aims during the initial stages of the conceptual design of engineering system， and use GA to find the solution for it. This method boosts the efficiency and precision of system reliability apportionment through exerting the ability of GA&FL. The simulation result shows the performance and feasibility of the new method.