Automatic monitoring of group-housed pigs in real time through porcine acoustic signals has played a crucial role in automated farming. In the process of data collection and transmission, acoustic signals are generally interfered with noise. In this paper, an effective porcine acoustic signal denoising technique based on ensemble empirical mode decomposition (EEMD), independent component analysis (ICA), and wavelet threshold denoising (WTD) is proposed. Firstly, the porcine acoustic signal is decomposed into intrinsic mode functions (IMFs) by EEMD. In addition, permutation entropy (PE) is adopted to distinguish noise-dominant IMFs from the IMFs. Secondly, ICA is employed to extract the independent components (ICs) of the noise-dominant IMFs. The correlation coefficients of ICs and the first IMF are calculated to recognize noise ICs. The noise ICs will be removed. Then, WTD is applied to the other ICs. Finally, the porcine acoustic signal is reconstructed by the processed components. Experimental results show that the proposed method can effectively improve the denoising performance of porcine acoustic signal.