The observation of airborne electromagnetic (AEM) system not only includes the response of the underground media but also comprises various kinds of noise. The motion-induced noise is the main source of AEM system with the characteristics of lower frequency, higher amplitude and non-periodicity. The ensemble empirical mode decomposition (EEMD) method is an effective method for random signal decomposition which decomposes the signal into N-level intrinsic mode functions (IMF) components and residual component. The high level IMF component of low frequency is used to fit the motion-induced noise, and the noise-free signal can be obtained by reconstructing the remaining IMF component and the residual component. In this study, the authors used EEMD method to distinguish and suppress motion-induced noise for both the simulation data and the survey data, and compared the denoising result between the EEMD method and the traditional spline method. The comparison result shows that the EEMD method can remove the motion-induced noise effectively due to the high fitting ratio and thus can get higher signal-to-noise ratio.