The core excitation saturation and vibration caused by DC bias are one of the important considerations in the design of high-frequency transformer (HFT). This paper studies the electromagnetic vibration characteristics of DC biased HFT with different winding structures. The vibration mechanism of iron core and winding under DC bias is analyzed. The optimal topology size of HFT is determined by area product (AP) method. In addition, the electromagnetic vibration multi-physical coupling model of a 500 V HFT under DC bias is established. At the same time, the electromagnetic vibration characteristics of interleaved winding and continuous winding of HFT are compared. The research shows that the current fluctuation of interleaved winding is smaller than that of continuous winding because of its ability to withstand impulse voltage. In addition, the average loss and maximum vibration displacement of HFT with entanglement winding are reduced in different degrees. The above research rules have guiding significance for the design of HFT and the method of suppressing DC bias.