With the development of high-frequency power conversion technology, the influence of the parasitic parameters of the transformer on the converters have become increasingly serious, hindering the development trend of high-frequency converters. In this paper, the operation process of the two-transistor flyback converters is divided into multiple stages, and parasitic parameters are also considered. The variations in the energy stored in the stray capacitance and the influences of stray capacitance on the converter are analyzed in detail in each stage. Four types of high-frequency high-voltage transformers with different winding structures and arrangements are designed and manufactured. The inner-primary-winding capacitances (stray capacitance of the primary winding) of the four transformers are estimated by calculating the electric field energy storage, and the electric energy storage of the four transformers are compared in detail. The influence of winding structures and arrangements on stray capacitance and the operation of converter are verified based on a two-transistor flyback converter with high input and low output voltages.