Unsteady aerodynamic characteristics of the wing with flaperon flying over nonplanar ground surface are investigated using a boundary-element method. The time-stepping method is used to simulate the wake shape according to the motion of the wing and flaperon over the surface or in the channel. The aerodynamic coefficient according to the periodic motion of the flaperon is shown as the shape of loop. The rolling moment coefficient of the wing flying in the channel is same as that of the wing flying over the ground surface. The variation range of pitching moment is wider when the wing flies in the channel than over the ground surface. The present method can provide various aerodynamic derivatives to secure the stability of superhigh speed vehicle flying over nonplanar ground surface using the present method.