This paper proposes a Model Predictive Control (MPC) method incorporating a drag adaptive mechanism for amphibious vehicles equipped with dual water jet thrusters, addressing the challenges of time-varying fluid resistance and strong nonlinear coupling during water motion. A three-degree-of-freedom hydrodynamic model (longitudinal, lateral, yaw) is established, explicitly considering the force configuration of the dual thrusters. The navigation resistance is abstracted as a piecewise function, transitioning from speed-proportional at low speeds to constant at high speeds, and a drag coefficient calculation method is integrated for adaptive compensation. Simulation results demonstrate the controller’s effectiveness: the vehicle successfully tracks multiple waypoints with stable speed, achieves desired longitudinal velocity with minimal overshoot, and controls the heading angle effectively.