In order to solve the problem of common mode interference that affects the accuracy of data acquisition system in industrial field, the manifestation of AC common mode interference is studied by means of waveform analysis, and its typical characteristics of DC offset superimposed AC fluctuation and background noise are revealed. It is proposed to characterize the interference intensity by the amplitude of the effective value of the waveform, and quantitatively express the common mode rejection ratio (CMRR). At the same time, the effect of the system background noise is eliminated by using the effective value superposition model, which improves the measurement accuracy of the common mode rejection ratio. Based on this method and process, the main sources of uncertainty, such as signal source error, data acquisition system gain error, amplitude measurement error, amplitude resolution error and measurement repeatability, are discussed. The measurement uncertainty is analyzed and evaluated. Combined with an example, the uncertainty evaluation result of channel CMRR is given, and the practicability and feasibility of the method is verified.