In this paper, we propose a hybrid modeling method for analyzing the electromagnetic compatibility characteristics of printed circuit boards (PCBs). The method uses an equivalent magnetic dipole array deduced from near-field scanning results obtained at a certain height over the PCB surface under test and the finite-difference time domain (FDTD) algorithm. The array of dipoles can simulate the PCB electromagnetic emissions, including the ground plane effect at a particular high frequency; the equivalent dipole array can then be imported into the FDTD calculation space for calculating the electromagnetic fields generated by the dipole array. In our experiment, we obtained the tangential magnetic field distribution of the PCB surface using near-field scanning, from where the tangential magnetic field component, orientation, and the magnitude and phase of the dipoles could be deduced. We used the proposed method to model two different modules on a highly integrated circuit. The results of the proposed method and those obtained by near-field scanning are nearly the same, which demonstrates the effectiveness and accuracy of the proposed method. We therefore conclude that the proposed modeling approach presents a new technique for studying the electromagnetic interference of PCBs.