The interaction of information during the structural design of aircraft is complex. In order to optimize the design process and improve the efficiency in research and development, this paper performs clustering calculation on the structural design matrix of a certain type of trainer and optimizes it through genetic algorithm. In addition, a specific method for calculating the amount of information through information connection weight is given. The simulation results show that the optimized matrix has strengthened the information interaction within the cluster, reduced the information interaction between clusters, and reduced the frequency of information feedback during the design process, which plays a role in improving the efficiency of research and development.