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• Combine VMD and whale optimization algorithm for noise reduction of MCG signal. • Adaptive optimization of the variational mode decomposition is performed. • Prevention of local optimum problems in optimization is performed. • Adaptive thresholding is used to denoise the decomposition results. • The algorithm was evaluated with simulated and measured signals. In the diagnosis and treatment of cardiac diseases, magnetocardiography (MCG) technology is characterized by non-invasive, non-contact, and high precision. Therefore, it has currently become a research hotspot in the field of new medical technologies. However, due to the weak signal of the magnetocardiography, the noise needs to be filtered after acquisition. In this paper, an optimized variational mode decomposition algorithm based on the improved threshold method and the improved whale optimization algorithm (WOA) is proposed to process the MCG signal. In order to improve the denoising accuracy, the improved whale optimization algorithm, VMD algorithm, and the improved threshold method are combined. Firstly, the correlation coefficients are obtained by the improved whale optimization algorithm to decompose the IMFs, then the baseline drift is removed by using the moving average method for the low-frequency IMFs, and then the improved thresholding algorithm is applied to each IMF. Finally, the denoised signal is obtained by integration. Experimental tests show that the algorithm has good denoising performance compared with similar algorithms and can filter environmental noise as much as possible without changing the original signal information. The proposed method has the highest Signal-to-Noise Ratio improvement (SNR imp) and Correlation Coefficient (CC) and the lowest Percentage Root Mean Square Difference (PDR). Also, the method is validated in real MCG signal processing. The proposed algorithm can be applied in the field of signal denoising, and it has a wide range of application backgrounds. [ABSTRACT FROM AUTHOR]