This study reveals the operating risk of cable breaking when the TMS–ROV recovery is carried out beneath rough ocean waves. To release the negative impact of the support vessels vertical heave motion on the station-keeping and position tracking performance of TMS, a robust hierarchical control scheme for a hydraulic-driven winch-based active heave compensation (AHC) system is proposed based on the combination of a nonlinear model predictive control (NMPC) strategy, an integral sliding mode control (ISMC) scheme and a vessel heave motion prediction algorithm. The motivation of utilizing the ISMC-based internal level combined with the integral state transformation technique is given by the robust capability to eliminate the uncertainties, which provides the nominal model for NMPC-based external level to guarantee the optimal evolution satisfying the state and input constraints and resisting the dynamical hysteresis caused by the employed extremely long cable length for deep-sea operation. Comparative simulation studies contribute to the analysis of the surge in cable tension during the TMS–ROV recovery and demonstrate the superior tracking and heave compensation performance, strong robustness and constraint satisfaction of the proposal.