In this paper, a novel multi-loop nonlinear internal model control (IMC) strategy for multiple-input multiple-output (MIMO) systems is presented under the partial least squares (PLS) framework, which automatically decomposes the system into several univariate subsystems in the latent space. To formulate a nonlinear dynamic PLS framework, we propose an ARX-neural network (ARX-NN) cascaded structure, and incorporate it into PLS inner model. A gradient-based optimization approach is then provided to identify the parameter sets of the ARX-NN PLS model so that the plant-model mismatch is minimized. Furthermore, with perfect model, we show that the response of the closed loop system can be reduced to a simple linear IMC filter with the original system delay. The simulation results of a methylcyclohexane (MCH) distillation column from Aspen Dynamic Module, demonstrate the effectiveness of our approach in terms of disturbance rejection and tracking performance. (C) 2011 Elsevier Ltd. All rights reserved.