In this paper, a hybrid realization model is proposed for the controllers of autonomous underwater vehicles (AUVs). This model is based on the model-based systems engineering (MBSE) methodology, in combination with the model-driven architecture (MDA), the real-time unified modeling language (UML)/systems modeling language (SysML), the extended/unscented Kalman filter (EKF/UKF) algorithms, and hybrid automata, and it can be reused for designing controllers of various AUV types. The dynamic model and control structure of AUVs were combined with the specialization of MDA concepts as follows. The computation-independent model (CIM) was specified by the use-case model combined with the EKF/UKF algorithms and hybrid automata to intensively gather the control requirements. Then, the platform-independent model (PIM) was specialized using the real-time UML/SysML to design the capsule collaboration of control and its connections. The detailed PIM was subsequently converted into the platform-specific model (PSM) using open-source platforms to promptly realize the AUV controller. On the basis of the proposed hybrid model, a planar trajectory-tracking controller, which allows a miniature torpedo-shaped AUV to autonomously track the desired planar trajectory, was implemented and evaluated, and shown to have good feasibility.