In this paper, we propose a multi-layer fuzzy logic controller (MLFLC) for multi-input-multi-output (MIMO) systems. For the convenience of analysis, the structure of the multi-layer fuzzy logic controller is divided into multi-input-singleoutput (MISO) controllers. Each multi-input-single-output controller consists of many fuzzy logic controllers (FLC). In the fuzzy logic controller the linguistic rules are designed as a suction controller. A theorem shows that such fuzzy logic controller has a switching line. The results of analysis show that the multi-layer fuzzy logic controller has a switching manifold and its parameters are the scaling factors which normalize the input variables. Moreover, a theorem which shows the stability of the proposed multi-layer fuzzy logic controller can easily be formulated by properly selecting the denormalizing scaling factors. A cart-pole system with two links is used as an illustrated example for demonstration. The demonstrations also include the links controlled to track a set of desired trajectories. Simulation results show that the fuzzy control system is asymptotically stable, and the desired trajectories can be followed very closely.