Wireless power transfer (WPT) is an emerging technology deployed for a wide range of applications. Various design challenges need to be addressed at both circuit and system levels. However, the conventional modeling methods either require impractical assumptions or only focus on the coil-to-coil part. This article presents a system-level model for WPT applications, including all the critical interior blocks, such as power amplifier, transmitter coil, receiver coil, matching networks, and rectifier. An accurate characterization method is proposed to obtain the rectifier impedance as a realistic load condition. Then, through frequency harmonic analysis, the power capabilities along the power flow path are analytically derived for both the fundamental and higher order harmonic components. The system efficiency and the power loss at each block can be accurately estimated. As a result, this model can not only optimize the system performance, but also help improve the thermal design for WPT products. With the assistance of this improved model, a practical design methodology is introduced to optimize the system parameters. An experimental prototype is built to validate the proposed model and the design methodology. Good correlations are observed between the calculations and experiments in both the time-domain and frequency-domain results.