This paper focuses on developing a data-driven trajectory tracking control approach for autonomous underwater vehicles (AUV) under uncertain external disturbance and time-delay. A novel model-free adaptive predictive control (MFAPC) approach based on a fuzzy state observer (FSO) was designed to achieve high precision. Concretely, the mathematical model of AUV motion was analyzed, and simplified via model decoupling, thus providing the model basis with an explicit physical explanation for the controller. Second, the MFAPC scheme for a multiple-inputs and multiple-outputs (MIMO) discrete time system was derived, that estimates system external disturbance. The controller can online estimate and predictive time-varying parameter pseudo-Jacobian matrix (PJM) to establish equivalent state space data-model for AUV motion system. Third, the Takagi–Sugeno (T–S) fuzzy model based state observer was designed to combine with the MFAPC scheme for the first time, which was used to online decline the state error generated by system uncertain time-delay. In addition, the stability of the proposed control scheme was analyzed. Finally, two trajectory tracking scenarios were designed to verify the effectiveness and robustness of the proposed FMFAPC scheme, and the simulations are implemented using the realistic parameters of T-SEA AUV.