This article presents a decentralized control strategy for the balancing of the cell voltages of a flying capacitor multilevel converter, implementing a large number of cells to address a high conversion ratio. The originality of this article is that no reference is required for regulating the capacitor voltages leading to an auto-balance capability. It is composed of several local cell-voltage balancing controllers and a global load-current regulator. For theoretical analysis purposes, a change of state variables is proposed, leading to a new model of the converter. Then, the study of the decentralized balancing method is performed based on a modal analysis of the system. A decoupling of the output current regulation and the cell-voltage balancing loops is proposed, and then observed. The synthesis of the controllers, guaranteeing the stability of the system within a large bandwidth for each mode, is obtained. To address the fault-tolerance requirement, this decentralized control strategy provides an opportunity for auto-reconfiguration, allowing changes in the number of active cells during operation. Simulations of the separated modal responses show the stability and bandwidth of the control loops for dc/dc 500 to 16 V high conversion ratio applications. Experimental results, performed on a 5-cell multilevel converter, demonstrate the validity of the proposed control method.