This article presents a nonlinear equivalent circuit model of an isolated dc-dc converter with a 3-phase medium frequency transformer. The model takes into account the magnetic cross saturation of the 3-phase core-type magnetic circuit. The model is suitable in detailed electromagnetic transient simulations of power systems involving isolated dc-dc converters. The model is developed using the Lagrange energy method. It involves a matrix of dynamic inductances containing a nonlinear term resulting from core magnetization and a linear term resulting from leakage flux. The model parameters are determined based on a series of magnetostatic finite element method simulations. This approach is convenient when applied to high power transformers offering a limited characterization effort, or if the transformer prototype does not exist. The experimental validation performed on a novel 3-phase MFT prototype in a 100 kW 1.2 kV 20 kHz dual active bridge converter has proved the validity of the model and model parameters. The no-load steady-state and inrush tests and the full-load test show a very good fit between the simulated and experimentally measured waveforms. The comparison with a classical simplified model neglecting magnetic cross saturation shows a significant difference in the no-load inrush test.