This work investigates the scattering characteristics of the rudder structure of aircraft considering electromagnetic discontinuities through multi level fast multipole algorithm (MLFMA) of the computational electromagnetics. Firstly, the scattering characteristics of the rudder seam and its influence on the omnidirectional radar cross section (RCS) are performed. Based on the traditional high-frequency analysis theory, the source and spatial contribution distribution of seam scattering are further studied. Numerical results demonstrate that the sidewall of the rudder seam is an important scattering source, and the radar absorbing material (RAM) coated on the sidewall of the seam has a good RCS reduction effect. In addition, this work presents the influence of the rudder deflection on the stealth performance, analyzes the effect of the rudder movement of the ordinary aileron and the split drag rudder on the scattering characteristics of the whole aircraft. The common aileron has little effect on the stealth performance of the aircraft, and it only causes scattering peak in the direction opposite to the control surface. However, the split drag rudder has great damage to the opposite direction stealth performance of the aircraft. When its deflection angle is 45°, the mean value of the opposite direction RCS increases by about two orders of magnitude compared with the deflection angle 0° state. The results indicate that the structure of aircraft rudder has a significant impact on the RCS characteristics of the whole aircraft.