Accurate loss evaluation of high-frequency transformers (HFTs) under non-sinusoidal excitation is essential for the optimal design of dual-active-bridge (DAB) converters, yet remains challenging due to spatially non-uniform magnetic flux distribution across the core and spectrally rich harmonic content in the winding current. This paper proposes a dual-refinement electromagnetic loss analysis method that combines a topology-aware region-partitioned improved generalized Steinmetz equation (IGSE) with a harmonic-resolved Dowell model. The ferrite core of a shell-type HFT is partitioned into three magnetically distinct zones—core legs, side pillars, and yokes—with the IGSE applied independently to each zone using zone-specific flux density waveforms derived from the single-phase-shift (SPS) control model, thereby capturing spatial non-uniformity in core loss. For winding loss, the current is decomposed via fast Fourier transform, and per-harmonic AC resistance is computed up to the seventh order with frequency-dependent skin depths, accounting for the spectral contribution to copper loss. A 300 V/6 kVA ferrite-core foil-winding HFT prototype was fabricated, and the proposed method was validated through COMSOL finite element simulations and experimental measurements using open-circuit and short-circuit tests. Results show that the calculated core loss and winding loss agree with measurements within 10–15% and 8–10%, respectively, demonstrating improved accuracy over the conventional uniform-IGSE and total-RMS Dowell approaches.