Heave compensation systems are essential for operations' safety, reliability, and efficiency in harsh offshore environments. This paper investigates the vibration suppression problem of a type of deep-sea robot with the length of time variation and harsh operating environments for active heave compensation systems, where hydraulic heave compensators implement actuators with input nonlinearity, model coupling, and unknown nonlinear disturbances. A robust adaptive output feedback control scheme based on the backstepping control method is designed to eliminate deep-ocean robot vibration, where the adaptive law handles the system parameter uncertainty. Meanwhile, a nonlinear disturbance observer (NDO) is introduced to overcome the effects of random disturbances and model coupling. In addition, the stability of the whole system is proved according to Lyapunov's theory, and the scheme is shown to be feasible by theoretical analysis. Finally, a comparative simulation study was conducted to validate the effectiveness of the proposed controller.