This study evaluates a sea-skimming cruise missile tracking control system using higher order sliding mode(HOSM) control based on an adaptive disturbance ob- server. Feedback control with finite time convergence was realized using a HOSM controller and differentiator. To increase the robustness of the control system, an adaptive disturbance observer was utilized to compensate for marine disturbances and aerodynamic fluctuations. These disturbances are merged into the unmatched external disturbance via the transformation of the cruise missile dynamics. A simulation was performed under various sea conditions to verify the high accuracy tracking and the robustness of the proposed scheme.