The invention relates to the field of electromagnetic compatibility, in particular to a system and a method for modeling printed circuit board level conducted electromagnetic interference. Conducted interference of a power wire port of a certain control circuit board is quantitatively analyzed by extraction through a circuit model and modular modeling. Interference noise sources, equivalent resistance R, inductance L, capacitance C, conductance G parameters and internal logic circuits of devices are acquired by respectively calculating and equalizing circuits, main interference chips, power modules and the like on the circuit board, modular package is performed, so that an equivalent circuit model of the whole power system is built, and conducted interference waveforms and quantitative spectra of points on a power wire can be obtained by circuit simulation. Conducted electromagnetic interference frequency and amplitude of key circuits on the printed circuit board can be quantitatively analyzed at a pre-design phase, portions with poor electromagnetic compatibility are found and optimized, the electromagnetic interference degree of the whole circuit board is reduced, and research and development cycle and cost can be reduced.