Morphing wing unmanned aerial vehicle (UAV) can satisfy multitask requirements, and is a tendency for future UAV. When morphing wing extending or shrinking, aerodynamics and moments vary largely, so a kind of robust controller is needed to satisfy the transitional process. This paper brings out LQG controller which can solve above problems. Firstly, affine nonlinear model of morphing UAV was dealt with, the LQG controller was designed for this linear model, at last, simulation was realized for morphing wing UAV, and control policy was analyzed, thus LQG controller was proved to be valid and robust.