This paper proposes a hybrid propulsion-based small underwater robot for robust trajectory tracking control in a harsh and complex underwater environment. The robot is equipped with a Coanda-effect jet thruster and a pair of propeller-based reconfigurable magnetic-coupling thrusters, allowing it to traverse safely in confined or cluttered spaces as well as cruise efficiently in the open water. To investigate the robot dynamic modeling, we first formulated its simplified mathematical model and estimated the hydrodynamic coefficients by performing the planar motion mechanism using CFD (computational fluid dynamics) simulation. Then, a double-loop trajectory tracking control architecture was designed considering the model uncertainties and environmental disturbances. Based on Lyapunov theory, the outer-loop kinematic control produces the virtual velocity command, while the inner-loop dynamic control adopts the full-state feedback L1-adaptive control to match the command. The asymptotic convergence of the tracking errors and the stability of the whole closed-loop system are guaranteed. Finally, comparative simulations in the presence of unknown disturbances and the variation of model parameters were carried out to verify the robustness of our proposed trajectory tracking control, which is also suitable for the separated son robots.