Most flying-wing aircrafts are static and dynamic unstable due to the lack of conventional stabilizers to control the plane in the longitudinal and the lateral directions, and the lateral-directional motion of the static instability flying-wing will cause the coupled longitudinal motion, so the control system is more complicated to design. With this motivation, the longitudinal and lateral-directional coupled motion of a longitudinal static instability flying-wing is modeled and analyzed. To guarantee a safe, airworthy flying-wing aircraft and decrease the design workload, the intelligent optimal seeking method based on the distributed genetic algorithm (DGA) was used to design the control system automatically and efficiently. The simulation results show the validation and efficiency of the DGA in the longitudinal and lateral-directional coupled control system design of the longitudinal static instability flying-wing aircraft. The analysis and optimal algorithm used in this paper will produce a direct benefit in relation to the flying-wing aircraft coupling characteristics analysis, the intelligent optimal method and the flying-wing aircraft flight control system design.