Considering the problem that the same frequency interference is easy to occur between the radar signals transmitted by the shipborne radar with same type in the complex battlefield environment, we design a frequency modulation (FM) coded signal with orthogonal characteristics. The search direction of conventional waveform coding with the orthogonal characteristic is improved, and the hybrid genetic chicken swarm optimization (HGCSO) is used to identify the coding sequences with low autocorrelation and low cross correlation characteristics. We adopt the back-learning chicken swarm algorithm to search the optimal values, and introduce the learning factor and the idea of mutation and crossover in genetic algorithm to update the individuals. A comprehensive evaluation of set pair analysis is used in fitness function, and the search direction is guided according to the relational degree of setting pair analysis to get a FM coding sequence pulse signal with excellent orthogonality. The fuzzy function of the obtained radar signal, the matched filtering of the echo signal, and the orthogonality of the simulation signal at different radar numbers are simulated respectively, and the results of simulations show that the FM coded signal designed by this algorithm can effectively resist the same frequency interference.