Abstract Electrocardiogram (ECG) is the most extensively applied diagnostic approach for heart diseases. However, an ECG signal is a weak bioelectrical signal and is easily disturbed by baseline wander, powerline interference, and muscle artefacts, which make detection of heart diseases more difficult. Therefore, it is very important to denoise the contaminated ECG signal in practical application. In this article, an effective ECG segments denoising method combining the ensemble empirical mode decomposition (EEMD), empirical mode decomposition (EMD), and wavelet packet (WP) is designed. The ECG signal is decomposed using the EEMD for the first time, and then the highest frequency component is decomposed by the EMD for the second time, and the high frequency components obtained from the second time are decomposed and reconstructed by the WP for the third time. Finally, the processed signal components are fused to obtain the denoised ECG signal. Furthermore, the signal‐to‐noise ratio (SNR), mean square error (MSE), root mean square error (RMSE), and normalised cross correlation coefficient (R) are used to evaluate the noise reduction algorithm. The mean SNR, MSE, RMSE, and R are 5.7427, 0.0071, 0.0551, and 0.9050 in the China Physiological Signal Challenge 2018 dataset. Compared with others denoising methods, the experimental results not only exhibit that the SNR of the ECG signal is effectively improved, but also show that the details of the ECG signal are fully retained, laying a solid foundation for the automatic detection of ECG segments.