Flying-wing configuration aircraft has multi-control-effectors redundantly. Especially the innovative drag rudders are implemented on it. So the control allocation is strongly nonlinear and multi-axes coupling. The features and applicability in different flight tasks of several typical control allocation methods were summarized. The multi-objectives optimization method based on nonlinear programming was utilized because of the new characteristics of the control allocation for the flying-wing configuration aircraft. The differences of control allocation results under different objectives were analyzed. And the attitude-tracking flight control system based on nonlinear dynamic inverse theory was designed, and the digital simulation using a six degree-of-freedom nonlinear model of certain flying-wing configuration aircraft was conducted, which demonstrate the applicability for flying-wing configuration aircraft. The results also indicated that the impacts of different optimizing objectives on flight states were remarkable and different.