This paper addresses the dynamic characteristics of an underwater towed system under manipulations of synchronous hydrofoils, considering the coupling of instantaneous fluid forces on the complete systems and hydrofoil control, which is usually difficult to solve with existing methods. A hydrodynamic model coupled with hydrofoil control algorithms is presented, wherein the hydrodynamic forces on the hydrofoils and Underwater Towed Vehicle (UTV) are simulated using the Computational Fluid Dynamics (CFD) method, and the fluid forces on the Towing Cable (TC) are described using a flexible cable dynamic model. The dynamic behaviors of the underwater towed system under depth-undulating, depth-tracking, and depth-keeping controls of hydrofoils are analyzed using the proposed model. The results show that the towing speed has a significant effect on the control efficiency of the hydrofoils. The dynamic responses of the underwater towed system increase or decrease more significantly in submerged depth control operations than in freely towing operations. The hydrofoils can achieve satisfactory effects in submerged depth control for the UTV at an appropriate towing speed, whereas it fails at a lower towing speed and noticeable dynamic response oscillations occur simultaneously. This study is expected to provide guidance on both hydrodynamic and control issues of underwater towed systems.