A higher frequency helps to design a compact wireless power transfer system. Due to the parasitic effects and component nonlinearity, the increased frequency would depreciate the accuracy of the circuit model (CM). The scattering parameters (SPs) are powerful to avoid this issue and helpful to study the efficiency and voltage gain. However, the existing SP-based analysis would fail when the nonstandard terminal impedance is used. This article explores the limitation of the original SP-based analysis and, then, proposes a modified one with the help of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\bm{ABCD}$</tex-math></inline-formula> and impedance matrices. For a system with a clear model, the modified SP-based analysis can get exactly the same results as the CM-based one in terms of calculation. In the experiment, a 1-MHz inductive power transfer system is built to show the benefit of the SP-based analysis with increased model uncertainty. Compared to the CM-based one, the largest error reduction is 17% for the efficiency and 8% for the voltage gain.