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The grounded electrical source airborne transient electromagnetic (GREATEM) system is an important method for obtaining subsurface conductivity distribution as well as outstanding detection efficiency and easy flight control. However, there are the superposition of desired signals and various noises for the GREATEM signal. The baseline wander caused by the receiving coil motion always exists in the process of data acquisition and affects measurement results. The baseline wander is one of the main noise sources, which has its own characteristics such as being low frequency, large amplitude, non-periodic, and non-stationary and so on. Consequently, it is important to correct the GREATEM signal for an inversion explanation. In this paper, we propose improving the method of ensemble empirical mode decomposition (EEMD) by adaptive filtering (EEMD-AF) based on EEMD to suppress baseline wander. Firstly, the EEMD-AF method will decompose the electromagnetic signal into multi-stage intrinsic mode function (IMF) components. Subsequently, the adaptive filter will process higher-index IMF components containing the baseline wander. Lastly, the de-noised signal will be reconstructed. To examine the performance of our introduced method, we processed the simulated and field signal containing the baseline wander by different methods. Through the evaluation of the signal-to-noise ratio (SNR) and mean-square error (MSE), the result indicates that the signal using the EEMD-AF method can get a higher SNR and lower MSE. Comparing correctional data using the EEMD-AF and the wavelet-based method in the anomaly curve profile images of the response signal, it is proved that the EEMD-AF method is practical and effective for the suppression of the baseline wander in the GREATEM signal. [ABSTRACT FROM AUTHOR]