<p>The integrated systems of unmanned surface vehicles (USVs) and remotely operated vehicles (ROVs) have been extensively applied in marine exploration and seabed coverage. However, the simultaneous navigation of USV-ROV systems is frequently limited by strong disturbances induced by waves or currents. This paper develops a novel rigidflexible coupling multibody dynamic model that incorporates disturbances of variable-length marine cables with geometrically nonlinear motion. A hybrid Lagrangian-Eulerian absolute nodal coordinate formulation (ANCF) element is developed to accurately model subsea cables which undergo significant overall motion, substantial deformation, and mass flow during the deployment of underwater equipment. Furthermore, the governing equations of the coupled USV-umbilical-ROV system are derived, considering wave-induced forces and current disturbances. A numerical solver based on the Newmark-beta method is proposed, along with an adaptive meshing technique near the release point. After validating three experimental cases, the cable disturbances at both the USV and ROV ends—caused by ocean currents, heave motion, and simultaneous navigation—are comprehensively compared and evaluated. Finally, it is demonstrated that a PD controller with disturbance compensation can enhance the simultaneous navigation performance of USV-ROV systems.</p>