The influence on aerodynamic optimization of flying wing configuration is studied based on discrete adjoint method, which 10%, 0%, -10% stability margin are considered in the optimization process, respectively. The free-from deformation (FFD) technique is used to achieve the parametrization of surface unstructured grid, the control point of FFD is selected to serve as design variable, then flowfield and adjoint equation is solved to obtain objective values and residual, the sequential quadratic programming(SQP) algorithm is utilized to obtain the gradient of control points, the final configuration is obtained by multiple iteration. The results show that the adjoint optimization can evidently improve the maximum lift-to-drag ratio under the constraint of geometric thickness and moment trim, and the increment exceeds 8% at these three conditions. The increment of cruise lift-to-drag ratio appears to reduce with the increase of stability margin while lift coefficient is fixed, the lift-to-drag ratio can increase 5.08% when the stability margin is 10%. Therefore, the optimization with higher stability margin can reduce can reduce trim drag and increase cruising lift-to-drag ratio to improve the flight performance of flying wing.