As a common fault of transformer winding, inter-turn short circuits cause severe consequences, such as excessive current and serious deformation of winding. Aiming to solve the problem of inter-turn short circuit at the end-winding and middle-winding of high frequency transformers (HFT), this paper considers the electromagnetic vibration characteristics of inter-turn short circuits (interleaved winding and continuous winding) at different positions, and the HFT is established by the multi-physical field coupling principle. Coupling equations for the inter-turn short circuit, as well as electromagnetic force and sound pressure level, are established to characterize the vibration noise mechanism of inter-turn short circuits. Furthermore, the HFT equivalent model is simulated in 3D finite element method (FEM) to emulate the real transformer operation and investigate the impact of interleaved winding and continuous winding under inter-turn short circuit faults. The short-circuit current and axial flux leakage, as well as the harmonic response of vibration acceleration and sound pressure level distribution, are obtained when inter-turn short circuits occur at different positions. Finally, the results show that the electromagnetic effect of the inter-turn short circuit in end-winding is worse than it is in middle-winding. Advantages in resisting impulse current make interleaved winding superior to continuous winding in terms of vibration and noise.