A novel online hybrid direct/indirect adaptive Petri fuzzy neural network (PFNN) controller with stare observer for a class of multi-input multi-output (MIMO) uncertain nonlinear systems is developed in the paper. By using the Lyapunov synthesis approach, the online observer-based tracking control law and the weight-update law of the adaptive hybrid intelligent controller are derived. According to the importance and viability of plant knowledge and control knowledge, a weighting factor is utilized to sum together the direct and indirect adaptive PFNN controllers. In this paper, we prove that the proposed online observer-based hybrid PFNN controller can guarantee that all signals involved are bounded and that the system outputs of the closed-loop system can track asymptotically the desired output trajectories. An example including four cases is illustrated to show the effectiveness of this approach.