Functionally graded materials (FGMs) have been proposed to be potential structural materials applied in high-speed spacecraft and power generation industries. In this study, an interface shape optimization method for designing FG sandwich structures with two different materials is proposed to minimize the compliance of FG sandwich structures under the volume constraint. Using the material derivative and adjoint methods, the shape gradient function is derived to determine the optimized interface shapes between different materials in FG sandwich structures without requiring shape design parameterization. FG sandwich structures with two sets of metal–ceramic materials, aluminum–alumina and aluminum–zirconia, are given as examples to verify the validity of the proposed optimization method, respectively. The results show that the compliance of FG sandwich structures with large difference between Young’s modulus of the component materials can be significantly reduced after optimized by the proposed method.