The interfere of body to lift face could not ignored in the influence of the flutter performance of the whole missile with large fineness ratio. The unsteady aerodynamic of lift face was computed using kernel function method, and unsteady lift coefficient was compared between only lift face and lift face with interfere of the body, then the general aerodynamics of whole missile was computed in the modal coordinates; it was found that difference was obvious. The flutter of the whole missile indicates that the interfere of body can not ignored in calculating the unsteady aerodynamics and the flutter of the whole missile, the interfere of body improves the flutter critical velocity of the whole missile.