When the winch traction system of a carrier-based aircraft works under complex sea conditions, the rope and the tire forces are greatly changed compared with under simple sea conditions, and it poses a potential threat to the safety and stability of the aircraft’s traction system. The accurate calculation of the rope and tire forces of a carrier-based aircraft’s winch traction under complex sea conditions is an arduous problem. A novel method of dynamic analysis of the aircraft-winch-ship whole system under complex sea conditions is proposed. A multiple-frequency excitation is adopted to describe the complex sea conditions and the influences of pitching amplitude, and the rolling frequency on the traction dynamics of a carrier-based aircraft along the setting trajectory under complex sea conditions are studied. The advantages and disadvantages of a winch traction system with trajectory control and without trajectory control in complex sea conditions are analyzed. For realizing the trajectory control of the aircraft, the vector difference between the center of mass for the carrier-based aircraft and the position on the predetermined Bessel curve is calculated, so as to obtain the azimuth vector in the aircraft coordinate system. This research is innovative in the modeling of the whole system and the trajectory control of a carrier-based aircraft’s winch traction system under the complicated sea condition of the multi-frequency excitation. ADAMS (Automatic Dynamic Analysis of Mechanical System) is used to verify the correctness of the theoretical calculation for the winch traction. The results show that the complex sea environment has a certain influence on the winch traction safety of the aircraft; in the range of 10–15 s for the traction, the rope force amplitude of complex sea conditions under the multi-frequency excitation is 29.5% larger than that of the single-frequency amplitude, while the vertical force amplitude of the tire is 201.1% larger than that of the single-frequency amplitude. This research has important guiding significance for the selection of rope and tire models for a carrier-borne aircraft’s winch traction in complex sea conditions.