In this paper, an extended state observer (ESO)- based controller with a model predictive governor is designed for 3D trajectory tracking of underactuated underwater vehicles. The proposed control scheme takes three primary challenges in cluding underactuated property, velocity constraint, and lumped disturbance into consideration. With respect to the model predic tive governor, an underactuated kinematic tracking error model is utilized to produce reference velocities. Meanwhile, a heading angle compensation mechanism is utilized to avoid the steady tracking errors resulting from dynamics coupling of the vehicle. Besides, an ESO is designed to estimate the lumped disturbances and unmeasured velocity states. Based on the ESO, a kinetic controller is offered to accomplish the precise velocity tracking only in virtue of the position and orientation information. Note that this paper details both the design process of the control scheme and rigorous theoretical analysis. Eventually, simulation and experimental results demonstrate the feasibility and superiority of the proposed method. Notably, this work lays the foundation for the underactuated trajectory tracking control in complicated and turbulent underwater environments