For the control allocation problem of flexible fly-wing aircraft with multi-control surfaces, the machine vibration force index was put forward to measure the elastic vibration. Total control allocation model was established, the superior performance of the Estimation of Distribution Algorithm (EDA) was used for solving the model. Firstly the rudder structure was designed, the way of work and control capability of every aerodynamic rudder were analyzed, and the rudder functional configuration was built in accordance with the rudder control efficiency of redundant rudder, elevator aileron and aileron rudder in aerodynamic data. During the control allocation, main performance indices of control allocation were analyzed, the overall multi-objective optimal evaluation function was established, which combined with the equality and inequality constraints, and solved by EDA. The true distribution was estimated by establishing a probability model, during the evolutionary process of EDA, the rudder would be allocated according to the deflection efficiency, the optimal solution was got by combining with the optimization function. At last, the impact of aero wing flexibility on static control performance of the system was analyzed. After considering aeroelasticity, the overshoot and transition time are decreases. The flying quality of flying wing aircraft is significantly improved, the system efficiency is improved by at least 10% after optimization. The simulation results show that the EDA can better solve the control allocation problem, and can improve the dynamic quality of the system, verifying the effectiveness of multi-control surfaces to control allocation.