The two-scale structure has the advantage of high specific strength, and optimizing the two-scale structure can greatly improve its performance. We propose an efficient M–VCUT (Multiple Variable Cutting) level set method to solve the topology optimization problem of the two-scale structures. The work is mainly divided into offline stage and online stage. In the offline stage, the geometric model of the microstructure was first established using the M-VCUT level set method; Then, the equivalent elastic modulus and density parameters of the microstructure were obtained using the homogenization method, and obtain the mechanical model of the microstructure. Then, the obtained parameters were stored and used as an offline database. During the online stage, the MQ-RBF (Multiquadric Radial Basis Function) interpolation technology is used to interpolation mapping model and using the mapping model for two-scale FEA (finite element analysis) and sensitivity analysis. This efficient method can solve the disadvantage of repeatedly calculating all finite elements in full-scale analysis and can greatly shorten the calculation time.