Aiming at improving the security of a semi-pelagic trawl in a complex working environment, this paper proposes a threedimensional tracking control system for the guidance of a semi-pelagic trawl on a complicated trajectory. The flexible nonlinear trawl system is simplified as a mass-spring-bar model. A hierarchical backstepping controller is then designed for the trajectory tracking of the trawl net and two otter boards. However, high-order state variables caused by the non-strict feedback characteristic of the trawl system appear frequently in recursive processes. Hence, a control algorithm based on the Sigmoid function is applied to construct the control outputs of these high-order variables. The stability of the proposed hybrid control method is analyzed based on the Lyapunov theorem when interference with an unknown upper limit occurs. Finally, simulation and contrast examinations show that the control algorithm is effective.