Optimization of meta-materials with the genetic algorithm is one of the most effective methods in the design of meta-materials in recent years. An integral system with interactive simulation of MATLAB and CST Microwave Studio is developed, and the main program of genetic algorithm is written in MATLAB with simulation and computation in CST to realize optimization of meta-materials by genetic algorithm with power of global optimization. Taking the compact second-order frequency selective surface optimization for example, the thinking of design is verified based on penalty function genetic algorithm, and a good effectiveness is obtained. Compared to the previous realizing way, this method is simple in programming operation，better in generality，and only needs a short circle design, simultaneously the method can be applied to other kinds of meta-materials.