In this work, to characterize the radiated emission from electronic circuits in shielding enclosure, an improved electric dipole-based source reconstruction method (SRM) is developed. Moreover, by resorting to this reconstructed equivalent source, the estimation of electromagnetic interference (EMI) between different circuit modules in the enclosure can be conveniently and accurately evaluated. Different from the free-space SRM, the equivalent dipoles of the proposed SRM are directly placed over the shielding box enclosed circuit board, and the numerical Green’s function (NGF) is developed to bridge the connection between the equivalent dipoles and the planar scanned magnetic near-field. With the NGF strategy, the effects of surrounding environments (including the presence of substrate, ground plane, and shielding enclosure) are inclusively considered, which makes the proposed SRM valid for any complex EM environments in theory. Since the proposed SRM also has the capability of reproducing the radiated emission inside the shielding enclosure, it is critically helpful to evaluate the EMI between different circuit modules inside the shielding enclosure. To reach this aim, the Rayleigh-Carson Reciprocity theorem is referred, in which the original EM coupling problem is decomposed into the “forward problem” and “reverse problem.” A Huygens box enclosing the victim circuit module is built and the EM fields on the box are obtained using the reconstructed dipoles in both problems. Then the EMI can be calculated accordingly. Therefore, the novelty and merits of the proposed approach are threefold: 1) the physically-based equivalent dipole model considers the interactions between the radiation sources and the surrounding objects, leading to the accurate prediction of radiated emissions both outside and inside the enclosure; 2) due to the utilization of the NGF, there is no approximation involved in the solution of the dipole’s radiation, thus improving the calculation precision; and 3) the near-field coupling between multiple electronic circuit modules inside the shielding enclosure can be identified precisely, which is useful for diagnostics of radiation sources. The effectiveness of this algorithm is verified by representative numerical examples.