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In order to study the effects of VFTO to transformers, the high frequency model for transformer windings must be set up. In this paper, a systematic methodology is presented for establishing the high frequency two-port circuit model of transformer windings under VFTO based on its frequency responses. The pi-equivalent circuit is constructed based on the Y-parameters transformed from the measuring S- parameters. A correction to the rational function of Y approximated by vector fitting (VF) is calculated, which enforces the real part of Y is positive definite. This enforcement can assure the passivity of the whole model, which could bring a stable simulation. The values of the synthesized RLCG elements can be easily calculated form the rational functions. This kind of pi-equivalent circuit model could do stable and exact simulation compared with the experiment results, which shows the validity of the method.