The relative motion control for the unmanned quadrotors autonomous shipboard landings is investigated in this study. The shipboard landing missions are divided into two phases including the position approaching phase and the vertical landing phase. Relative pose kinematics and dynamics are modeled in the quadrotor’s body-fixed frame, where the kinematic couplings resulted from the difference between ship’s centre of mass and desired landing site and the unknown external disturbances of two vehicles are considered in the modeling and control design. In the position approaching phase, because of the under-actuated property of quadrotors, the adaptive backstepping technique is combined with an auxiliary system and a command filter to develop the guidance and control laws. Subsequently, the relative altitude-attitude controller is designed for the vertical landing phase. Stability analysis shows that the position approaching errors in the first phase and the landing errors in the second phase ultimately converge to small neighborhoods of zero, and numerical simulation validates the effectiveness of the proposed strategy.