An adaptive disturbance rejection algorithm is proposed for carrier landing system in the final-approach. The carrier-based aircraft dynamics and the linearized longitudinal model under turbulence conditions in the final-approach are analyzed. A stable adaptive control scheme is developed based on LDU decomposition of the high-frequency gain matrix, which ensures closed-loop stability and asymptotic output tracking. Finally, simulation studies of a linearized longitudinal-directional dynamics model are conducted to demonstrate the performance of the adaptive scheme.