As electronic products become increasingly more complicated, multiple noise sources are likely to simultaneously interfere with the radio frequency (RF) receiver. It will be very helpful if the dominant noise source can be identified when solving the RF interference issue in a complex system. This article proposes a method to separately calculate the contributions from multiple noise sources at their overlapped frequencies so that the worse noise source could be identified even when multiple sources radiate simultaneously. The proposed method creatively employs the decomposition method based on the reciprocity theory to calculate the interference contribution from different sources. Furthermore, in the interest of reducing the near-field scanning time and complexity, the magnetic field only scanning method is developed by using the finite-element method (FEM). In the proposed method, Huygens's surface is established for each source. The tangential magnetic near fields on each Huygens's surface were then applied to solve the corresponding tangential electric fields by the FEM. Subsequently, the sources are removed while the corresponding Huygens's surfaces are maintained. The victim structure is excited under these conditions to obtain the tangential magnetic fields on Huygens's surfaces, and a novel FEM procedure is applied to obtain the tangential electric fields. Finally, based on the electric and magnetic fields, the interference from each noise source can be separately estimated based on the reciprocity theory. This method is validated by a numerical example and measurement. This approach can assist engineers in identifying the contribution of coupling from different sources and in efficiently resolving electromagnetic interference issues.