Air rudder system is a typical control part of aircraft, and its substructures, such as servo actuator, connecting rod, rocker arm, rudder shaft, and rudder surface, contribute to the overall stiffness of the air rudder system in different degrees. The overall stiffness of the air rudder system can be significantly optimized by reasonably allocating the stiffness of each substructure. An efficient stiffness allocation optimization method based on combination of transfer matrix method of multibody system and genetic algorithm is proposed in this paper. Firstly, an efficient structural dynamic model with structure sizes and material properties as parameters is established based on the transfer matrix method of a multibody system. The simulation results show that the error between the natural frequency of the first pitch mode predicted by the model and calculated by commercial software is only 1.06%. Secondly, based on the efficient structural dynamic model established in this paper, sensitivity analysis of contribution of the stiffness of each substructure to dynamic characteristics of the air rudder system is carried out, and the law of contribution of each component to the natural frequency of the system is given. Finally, combination of genetic algorithm and transfer matrix method of multibody system is adopted, and stiffness allocation of substructures is optimized by taking the established highefficiency structural dynamics model of the air rudder as the fitness function, the size of each substructure as the variable to be optimized, and the weight of the air rudder system as the constraint condition. The optimization results show that the natural frequency of the first pitch mode of the air rudder system can be increased by about 15.8% while keeping the overall weight of the air rudder system unchanged.