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This paper presents a novel nonlinear control strategy for a class of uncertain single-input and single-output discrete-time nonlinear systems with unstable zero-dynamics. The proposed method combines adaptive-network-based fuzzy inference system (ANFIS) with multiple models, where a linear robust controller, an ANFIS-based nonlinear controller and a switching mechanism are integrated using multiple models technique. It has been shown that the linear controller can ensure the boundedness of the input and output signals and the nonlinear controller can improve the dynamic performance of the closed loop system. Moreover, it has also been shown that the use of the switching mechanism can simultaneously guarantee the closed loop stability and improve its performance. As a result, the controller has the following three outstanding features compared with existing control strategies. First, this method relaxes the assumption of commonly-used uniform boundedness on the unmodeled dynamics and thus enhances its applicability. Second, since ANFIS is used to estimate and compensate the effect caused by the unmodeled dynamics, the convergence rate of neural network learning has been increased. Third, a “one-to-one mapping” technique is adapted to guarantee the universal approximation property of ANFIS. The proposed controller is applied to a numerical example and a pulverizing process of an alumina sintering system, respectively, where its effectiveness has been justified.