Abstract: Solid state transformer (SST) based on the magnetically coupled three-phase dual-active-bridge (DAB3) DC/DC converter is suitable for high-power applications. It is crucial for the elaborate design of SST to accurately estimate the copper loss and magnetic core loss of its key magnetic component—high-power three-phase medium-frequency transformer (MFT3) under nonsinusoidal voltage excitation, and it is also crucial to analyze its variation with operation modes and winding configurations. Based on the analysis of operation principle and equivalent circuit model of the DAB3 converter, the expressions of harmonic current of MFT3 with different winding configurations, including Y-Y, Y-Δ, Δ-Δ, are derived by using fundamental wave analysis. The influences of skin effect and proximity effect on AC resistance at each order harmonic frequency are considered to realize the calculation of copper loss. Considering the voltage waveforms and phase shift strategy under different winding configurations, the expressions of the piecewise linear magnetic flux density waveforms under six-step and three-step voltage waveform excitations are deduced, and the extended expressions of modification expressions of the Steinmetz equation are presented to determinate the magnetic core losses under different phase shift angles. Simulation and experimental results on 5 kHz/15 kW MFT3 model with nanocrystalline alloy core verify the effectiveness of the above methods.