A conducted EMI noise suppression method of a complex electronic system comprises: 1) analyzing the reasons generating the conducted EMI noise: (1) crosstalk, (2) bad grounding, and (3) PCB (printed circuit board) impedance mismatch; and 2) tightly winding the live wire and the neutral wire of a crosstalk choking coil in a negative-incoming negative-outgoing manner if the conducted EMI noise is caused by crosstalk; connecting capacitors (C1 to C8) in parallel, and respectively disposing U1 and U2 between C1 and C2, and between C4 and C5 if the conducted EMI noise is caused by bad grounding, wherein U1 is equal to U2, and the capacitances of C1, C2, C3, C4, C5, C6, C7 and C8 are respectively 22muF, 22muF, 0.1muF, 0.1muF, 0.1muF, 0.1muF, 100muF, and 10pF; and calculating the characteristic impedance of the PCB circuit by using electromagnetic simulation software, and carrying out signal integrity analysis according to the frequency characteristics of the transmission signal to realize the optimum impedance match of the PCB circuit if the conducted EMI noise is caused by PCB impedance mismatch.