In this paper, a topology optimization design method is proposed for high gain metamaterial cladding microstrip antenna based on genetic algorithm. Adopting a holistic approach to metamaterial elements and the maximum gain value of the microstrip antenna is selected as the objective function. The binary 0-1 coding of the lattice copper patch behind the discretization of the metamaterial copper-clad area is selected as the optimization variable. The topology optimization model of metamaterial microstrip antenna at 24 GHz is established. The redundant design method of patch square grid is used to eliminate the point connection phenomenon and a suitable genetic algorithm strategy is adopted to solve the optimal design problem of 10×10 square lattice size, thus obtaining a new metamaterial microstrip antenna without point connection. The results show that metamaterial cladding microstrip antenna has better matching performance compared with the conventional microstrip antenna, and its gain performance and directivity are significantly improved. Thereinto, the maximum gain performance is raised from 7.51 dB to 11.54 dB, and the improvement rate is 53.66%. Finally, the topological optimization design of metamaterial microstrip antennas with different square lattice sizes such as 12×12 and 14×14 is studied. The results show that the creative configuration design of the metamaterial microstrip antenna is convergent, and the microstructure configuration for 10×10 lattice size is the most cost-effective.