To design an electromagnetic interference (EMI) suppression filter for a switched mode power supply (SMPS) systematically, information of the noise source impedance and noise terminating load impedance is essential for selecting the most appropriate filter configuration and choosing the respective filter elements’ values. Based on a two-current-probe measurement approach, a novel method to determine both common-mode (CM) and differential-mode (DM) noise source impedance of an SMPS has been developed. The proposed method allows measurement of noise source impedance of an SMPS under its normal powered on condition. With proper premeasurement calibration, it is capable of deriving noise source impedance of SMPS in terms of equivalent electrical circuit model with good accuracy. Once the equivalent electrical model of the noise source impedance is derived through measurement, the most effective filter configuration and component’s value for the built-in EMI filter of the SMPS could be designed without the usual guessing approach.