The mechanical characteristics of the rudder structure have a critical impact on the flight performance of the aircraft, and these characteristics are governed by the structure’s geometric configuration. A topology optimization method for designing the metal powder particle damping composite rudder structure was proposed. The load-bearing function was satisfied by optimizing the stiffeners of the rudder structure and the vibration suppression was achieved by optimizing the position distribution of the powder particle dampers. The internal stiffener distribution of the rudder structure was determined via the adaptive growth method, while the equivalent performance of the powder particle damper was evaluated using the homogenization method. Based on the homogenized parameters, the position distribution of the powder particle dampers within the rudder was optimized to realize a collaborative design that concurrently addressed both load-bearing and vibration suppression functions. The simulation results show that, compared to the original rudder structure, the static mechanical performance of the optimized metal powder particle damping composite rudder structure is improved by 10.35%, the first natural frequency is increased by 22.10%, the frequency response at the first natural frequency is reduced by 22.88%, and the flutter speed is increased by more than 10% when the Mach number is 4, 5, 6. The proposed design method provides a new solution for the design of lightweight, high-rigidity structures with vibration suppression functions.