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The accurate extraction of high frequency impedance of the 3D complex interconnects depends mainly on calculation of the 3D eddy current problem. The purpose of this paper is to put forward a boundary integral equation model for calculation of the 3D eddy current problem, which employs two separate imaginary sources, distributed over the interfaces of different regions, and the scalar potential on these interfaces as unknowns. As a boundary element method, this model avoids volume discretization of the conductors and substrate, endowing it with a potential speed. advantage. This model can be used to calculate mutual impedance between two perpendicular conductors by discarding the assumption that the current flows only along the axis direction of the conductors. Furthermore, it is applicable to general 3D structures. The validity of the new model is verified by the numerical results from several simple examples.