This book focuses on water content estimation and control of the PEM fuel cell stack and the individual cell in vehicle. Firstly, the mathematical connection between polarization curve and equivalent circuit model proves importance of MEA and its feasibility to study water content. Optimizing structure of MEA realizes the internal water content recirculation of a fuel cell and improves its performance under middle or lower current density. The influence of water content on performance of MEA is quantified, and variation of equivalent circuit model is an excellent indicator of water content. Secondly, the comprehensive online AC impedance measurement method is put forward, including current excitation method, weak voltage and current signal processing method, and method for analyzing measurement error, and experiment validates measurement accuracy. The high-frequency impedance and statistical characteristic are proposed as indicator of water content. Finally, the dynamic model of the air supply system of a fuel cell engine is established and the closed-loop control of the air supply system and the water content estimation are decoupled. The experiment on a fuel cell system validates the proposed method for searching optimized operating conditions and the water management strategy.