Aerial rudders are significant actuators in the spacecraft control systems and are responsible for the stability and control of different motions such as pitching, yawing and rolling around mass center. With the development of new generation of space vehicles, high speed flight demonstration, light and thin aerial rudders with large span-chord ratio have been widely used. In the design of control strategies in pitching, yawing and rolling channels and control feedback loop parameters, the influence caused by aerial rudder elastic deformation should be considered particularly. In this paper, elastic motion equations of the spacecraft flexible rudder are studied firstly. Then, according to the modal vibration features, aerodynamic force derivative distribution characteristics and generalized force expressions, the rudder station division and computation method of generalized rudder aerodynamic force derivatives are proposed in the pitching, yawing and rolling channels based on the computational fluid dynamics simulation. By comparison the results of the proposed method with these of the traditional computation methods, the accuracy and validity of the proposed method are verified which can provide considerable references and basis in the control design of flexible rudder in the spacecraft.