Aiming at the problem of precise landing of carrier-based aircraft under complex marine environment conditions and improving the safety and accuracy of landing, a direct lift control method of carrier-based aircraft based on the decoupling of crosslinking coefficients is proposed. The control system of the carrier-based aircraft is optimally designed through the eigenstructure assignment method and the direct decoupling method of crosslinking coefficient. The eigenstructure assignment method can configure different eigenvectors and eigenvalues to suit the specific flight mission, effectively adjusting the dynamic characteristics of the aircraft to approximate system performance and meet decoupling requirements. The direct decoupling method of crosslinking coefficient establishes a relationship between flaps and elevators, so that the moment generated by the flap is eliminated by the elevator. Ultimately, simulation results validate the efficacy of these methods: eigenstructure assignment method intuitively configures mode poles for decoupling design, while crosslinking coefficient decoupling method realizes the adjustment of trajectory angle while maintaining a stable angle of attack (AoA). These methods are straightforward to implement and yield significant control effects.