Airplane flutter scale model should maintain the load transfer characteristics of the original structure. It is a structural inverse problem for proper natural frequencies as well as structural simplification. This inverse problem could be solved by topology optimization. So based on bi-direction evolutionary structural optimization (BESO) method, a topology method for designing fuselage flutter model is presented. Facing porous and irregular shape often appears in topology optimization, a regular shaped grid frame structure consisted of the finite elements is discussed, including its internal mapping relationship and boundary conditions. The ratio criterion for structural modification is raised in this structural topology optimization using frequency sensitivity. Finally, this topology optimization method is applied to cylindrical fuselage flutter model design, result shown that the proposed approach is feasible to achieve given natural frequencies, maintains the character of inner frame structure completely, and the similarity between optimized structure and original structure is achieved.